HIPAA Compliance Checklist: 2025 Guide for SaaS & HealthTech

Data privacy is not just a promise, it’s a legal obligation. The Health Insurance Portability and Accountability Act (HIPAA) sets the gold standard for protecting patients sensitive health information, and for SaaS providers and HealthTech startups, meeting HIPAA requirements is non-negotiable if you want to earn provider trust, secure partnerships, and avoid steep penalties.

According to the U.S. Department of Health and Human Services (HHS), HIPAA violations can result in fines of up to $1.5 million per year for each violation category – and settlements in recent years have exceeded $5 million for a single breach.

HIPAA compliance requires strong administrative, physical, and technical safeguards to protect sensitive health data and uphold patients’ rights. For SaaS companies and HealthTech startups, it’s essential for earning trust, securing partnerships, and avoiding costly penalties – especially as digital tools like cloud infrastructure and telehealth increase exposure risks. HIPAA covers two groups: Covered Entities (healthcare providers and health plans) and Business Associates (like SaaS vendors and IT partners) that handle PHI. This checklist helps SaaS, mHealth, and B2B health data processors protect patient data, stay compliant, and grow confidently in today’s digital healthcare landscape.

HIPAA Core Frameworks Explained

HIPAA is based on several interlocking frameworks that aim to safeguard confidential healthcare data. These are the Privacy Rule, Security Rule, Breach Notification Rule, and Enforcement Rule. Knowing how these rules are connected helps SaaS companies and HealthTech firms manage PHI responsibly and remain compliant in their growth journey.

Each framework addresses a distinct portion of the compliance puzzle. The Privacy Rule governs the use and disclosure of PHI. The Security Rule is concerned with the protective electronic and administrative measures for PHI. Breach Notification Rule specifies procedures for compromised data, whereas Enforcement Rule outlines compliance supervision and penalty application processes.

The 3 key safeguards: Administrative, Physical, Technical

HIPAA mandates a multi-layered approach to data protection, built on three core types of safeguards:

• Administrative Safeguards: Policies, procedures, and training programs that define how an organization manages and protects PHI. This includes conducting regular risk assessments, designating a HIPAA security officer, training the workforce, and developing contingency plans for data backup and disaster recovery.
• Physical Safeguards: Measures that protect physical locations and devices where PHI is stored or accessed. This includes controlling facility access with locks or security badges, securing workstations and devices, using surveillance systems, and properly disposing of hardware or media containing PHI.
• Technical Safeguards: Technology and processes used to protect electronic PHI (ePHI). Key elements include access controls (such as passwords and authentication), encryption, audit controls to monitor system access, and secure methods for data transmission.

The Privacy Rule vs Security Rule

• Privacy Rule: The HIPAA Privacy Rule sets standards for how PHI is used and disclosed, focusing on protecting patient rights and limiting who can access health information. It applies to all forms of PHI – electronic, paper, and oral – and gives patients certain rights over their health data, such as the right to access and request corrections.
• Security Rule: The Security Rule specifically addresses the protection of electronic PHI (ePHI). It requires covered entities and business associates to implement administrative, physical, and technical safeguards to ensure the confidentiality, integrity, and availability of ePHI.

HIPAA Breach Notification Rule

The HIPAA Breach Notification Rule requires covered entities and their business associates to promptly notify affected individuals, the U.S. Department of Health & Human Services (HHS), and in some cases the media if unsecured protected health information (PHI) is compromised. This notification must happen without unreasonable delay and no later than 60 days after discovering the breach.

Not every incident automatically counts as a breach. If you can prove – through a documented risk assessment that there’s a low probability PHI was compromised, notification may not be required. Having a clear plan for incident response, clear internal reporting, and thorough documentation helps organizations meet these requirements, limit the damage, and maintain patient trust when things go wrong.

Omnibus Rule and the role of Business Associate Agreements (BAAs)

The HIPAA Omnibus Rule, introduced in 2013, significantly expanded the scope and enforcement of HIPAA regulations. It clarified that business associates – vendors and partners who handle PHI on behalf of covered entities – are directly liable for HIPAA compliance. The Omnibus Rule also strengthened privacy protections and breach notification requirements.

A critical component of this rule is the Business Associate Agreement (BAA). Covered entities must have BAAs in place with all business associates. These contracts outline each party’s responsibilities for safeguarding PHI and ensure that business associates are held to the same compliance standards as covered entities. Without a valid BAA, sharing PHI with a vendor is a violation of HIPAA.

Pre-Compliance Readiness

Laying a solid foundation is essential before implementing HIPAA controls. Pre-compliance readiness is where SaaS and HealthTech companies map out how protected health information (PHI) flows through their systems, who touches it, and which vendors process it on their behalf.

Equally important, this stage aligns your people, processes, and tools. Assign clear ownership for compliance tasks, define who manages training and policies, and plan how you’ll track evidence like access logs and vendor agreements.

Appoint a HIPAA compliance officer

Designate a HIPAA compliance officer (or officers) to oversee your compliance program. This individual is responsible for:

• Developing and updating privacy and security policies.
• Managing and delivering HIPAA training to staff.
• Overseeing risk assessments and mitigation plans.
• Investigating security incidents and suspected breaches.
• Coordinating breach reporting and response.

Conduct an initial risk assessment

A comprehensive risk assessment is the cornerstone of HIPAA readiness. This process involves:

• Identifying all locations and systems where PHI is created, stored, processed, or transmitted
• Evaluating potential threats and vulnerabilities (e.g., unauthorized access, data loss, cyberattacks, insider threats).
• Assessing the likelihood and potential impact of each risk.
• Prioritizing risks and developing mitigation plans.

Identify all systems processing or storing PHI

Create a detailed inventory of all systems, applications, and devices that handle PHI. This includes:

• Electronic health record (EHR) platforms
• Cloud storage and SaaS solutions
• Mobile devices and laptops
• On-premises servers and backup drives
• Email and messaging platforms

Classify PHI and data flows

Not all data is created equal. Classify the types of PHI your organization handles (e.g., patient records, billing information, lab results) and map out how this data moves through your workflows. Use data flow diagrams to visualize:

• How PHI is collected, used, and shared internally
• Where PHI is transmitted to external partners or vendors
• Points where PHI is stored, archived, or disposed of.

Inventory your vendors and data-sharing partners

List every third-party vendor, business associate, and partner with access to your PHI or systems. For each:

• Determine if a Business Associate Agreement (BAA) is required
• Assess the vendor’s own HIPAA compliance status and security practices
• Document the nature and scope of PHI shared

HIPAA Compliance Checklist (2025)

Healthcare data is among the most sensitive information a company can handle – and for SaaS and HealthTech businesses, safeguarding that data isn’t just good practice, it’s a legal requirement. The Health Insurance Portability and Accountability Act (HIPAA) sets the standard for protecting protected health information (PHI) in the United States, and staying compliant is non-negotiable if you want to serve healthcare providers, payers, or patients.

This 2025 HIPAA Compliance Checklist breaks it all down step by step. It covers administrative safeguards, technical requirements, vendor management, secure implementation, and how to keep your compliance program strong over time.

Administrative Safeguards

Administrative safeguards form the backbone of any HIPAA compliance program. While technical and physical safeguards protect your systems and hardware, administrative safeguards ensure that your people, policies, and procedures work together to protect sensitive patient information every day.

For SaaS and HealthTech companies, administrative safeguards cover how your workforce is trained, how access is granted and revoked, how incidents are handled, and how you plan for unexpected events like data loss or breaches.

Workforce training and policies

Your team is often your biggest security risk – and your strongest line of defense. HIPAA’s Privacy and Security Rules require regular workforce training to ensure every employee understands how to handle PHI securely.

• Develop and document clear privacy and security policies that align with HIPAA requirements.
• Keep detailed records of all training activities, including dates, attendees, and content covered.

Contingency planning and DR testing

HIPAA requires organizations to have a contingency plan to protect and restore PHI in the event of an emergency or system failure. A solid contingency plan limits downtime and minimizes data loss during unexpected events such as ransomware attacks, natural disasters, or server outages.

• Develop a written contingency plan outlining steps for data backup, disaster recovery, and emergency operations.
• Test your disaster recovery and data restoration processes periodically to confirm they work as intended.

Sanction policies for HIPAA violations

Mistakes and negligence can happen – even in the most compliant organizations. HIPAA requires that you establish clear sanction policies for workforce members who fail to comply with your privacy and security policies.

• Draft a formal sanction policy detailing how violations are identified, investigated, and addressed.
• Apply sanctions consistently, with consequences proportionate to the severity of the violation – ranging from retraining to disciplinary action or termination for serious breaches.

Technical Safeguards

The 2025 HIPAA Security Rule introduces mandatory technical safeguards to address the evolving threat landscape and ensure robust protection of electronic Protected Health Information (ePHI). Below are the key technical requirements and best practices that every healthcare organization must implement to stay compliant.

Access controls (MFA, RBAC)

• Multi-Factor Authentication (MFA): MFA is now required for all remote access to systems containing ePHI. This significantly reduces the risk of unauthorized access, even if passwords are compromised. All staff logins must have MFA enabled, using authentication methods that meet current industry standards.
• Role-Based Access Control (RBAC): Access to ePHI must be limited based on job roles and responsibilities. Only authorized personnel should have access to the minimum necessary information needed for their duties, reducing the risk of internal breaches.

Encryption of data at rest and in transit

• Mandatory Encryption: All ePHI must be encrypted both when stored (at rest) and when transmitted across networks (in transit). This ensures that even if data is intercepted or stolen, it remains unreadable to unauthorized parties.
• Industry-Standard Protocols: Use strong, up-to-date encryption protocols such as AES-256 for data at rest and TLS 1.3 for data in transit to comply with HIPAA’s technical requirements.

Activity logs and audit trail setup

• Comprehensive Audit Logging: Systems must record all access and activity related to ePHI, including successful and failed login attempts, data access, modifications, and deletions.
• Real-Time Monitoring: Automated monitoring solutions should be in place to detect suspicious activities and potential breaches as they occur.
• Retention and Review: Audit logs must be retained for a specified period (typically six years) and regularly reviewed to identify anomalies or unauthorized access.

Automatic session timeouts and password policies

• Automatic Session Timeouts: Systems must automatically log users out after a period of inactivity to prevent unauthorized access from unattended devices.
• Strong Password Policies: Enforce the use of complex passwords and require regular password changes. Password policies should align with current best practices, such as minimum length, character complexity, and restrictions on password reuse.
• Person or Entity Authentication: Ensure that all users are properly authenticated before accessing ePHI, reinforcing the need for strong password management and MFA.

Physical Safeguards

Physical safeguards are a crucial component of the HIPAA Security Rule, focusing on the protection of physical access to facilities and devices that store or process electronic Protected Health Information (ePHI). These safeguards are designed to prevent unauthorized access, tampering, theft, and environmental hazards, ensuring the confidentiality, integrity, and availability of sensitive health data.

Facility access controls (badges, biometrics)

• Access Restriction: Limit facility access to only authorized personnel using security measures such as ID badges, biometric scanners, or security staff. This ensures that only individuals with legitimate business needs can enter sensitive areas where ePHI is stored or processed.
• Visitor Management: Implement policies for visitor access, including sign-in procedures, visitor badges, and escort requirements. All visitors should be logged and monitored during their stay.
• Access Validation: Regularly review and update access lists to ensure only current staff and authorized individuals retain access privileges.

Server cabinet locks and visitor logs

• Physical Security of Equipment: Secure servers and network equipment in locked cabinets or rooms. Only authorized IT staff should have access to these areas.
• Visitor Logs: Maintain detailed logs for all visitors who access sensitive areas, including the date, time, purpose of visit, and the person authorizing access. This documentation is essential for audit trails and incident investigations.
• Maintenance Records: Document any repairs or modifications to facility security components, such as locks, doors, or surveillance systems, to maintain a clear record of physical security measures.

Disaster recovery site readiness

• Contingency Operations: Establish and implement procedures that allow facility access in support of data restoration and emergency operations in the event of a disaster. This includes ensuring that backup sites are ready and accessible to authorized personnel.
• Regular Testing: Periodically test disaster recovery and emergency access procedures to confirm that critical systems and data can be restored promptly and securely.
• Facility Security Plan: Develop and maintain a security plan for both primary and backup sites, addressing risks from natural disasters, fire, and unauthorized access.

Documentation and Policy Templates

Having the right policies and documentation isn’t just a best practice – it’s a HIPAA requirement. Documentation shows regulators, auditors, and partners that you have clear processes in place to protect patient data and respond appropriately if something goes wrong. Following are three essential policy templates every SaaS or HealthTech company should maintain and customize.

HIPAA privacy policy

A well-crafted HIPAA privacy policy explains how your organization collects, uses, stores, and shares PHI. It should outline patient rights, your obligations, and how you handle requests for access, corrections, or restrictions.

• Write a clear, accessible privacy policy that aligns with HIPAA’s Privacy Rule.
• Include details about permitted uses and disclosures of PHI, patient rights, and how patients can file complaints.
• Make the policy easily available – for example, publish it on your website and provide it to patients and partners upon request.

Incident response plan

Despite best efforts, data breaches can happen. HIPAA requires covered entities and business associates to be ready with a clear plan for detecting, reporting, and responding to security incidents.

• Develop a written incident response plan that outlines roles, responsibilities, and escalation procedures.
• Define how to identify and contain incidents quickly to limit damage.

Employee access and training logs

HIPAA auditors often request proof that your workforce training happens as required – and that access to PHI is properly controlled and monitored. Maintaining up-to-date logs is crucial for demonstrating compliance.

• Keep detailed logs showing which employees have access to PHI, what level of access they have, and when that access was granted or revoked.
• Record all training sessions, including topics covered, dates, and participant signatures.

Vendor and BAA Management

Even if your internal teams follow every HIPAA rule, your compliance can still be at risk if a vendor mishandles PHI. That’s why the HIPAA Privacy Rule requires covered entities and business associates to have formal agreements and oversight processes for any third-party partners who access or process protected health information.

Review and sign BAAs with all PHI-handling vendors

A Business Associate Agreement (BAA) is a legally binding contract that outlines how your vendors will safeguard PHI in line with HIPAA requirements. Without a valid BAA in place, sharing PHI with a third party is a violation.

• Identify every vendor that creates, receives, maintains, or transmits PHI on your behalf such as cloud service providers, billing companies, EHR platforms, and support contractors.
• Review and negotiate BAAs to ensure they clearly define each party’s privacy and security obligations, permitted uses and disclosures, and breach notification responsibilities.

Ensure vendor HIPAA compliance attestation

A signed BAA alone doesn’t guarantee a vendor is actually following HIPAA best practices. You must also verify that business associates have the necessary safeguards in place.

• Request evidence of each vendor’s HIPAA compliance – such as a compliance attestation, audit summary, or relevant certifications.
• Confirm that vendors train their workforce on HIPAA requirements and have documented security and privacy policies.

Annual vendor access reviews

Vendor access to PHI shouldn’t be “set and forget.” Regular reviews ensure that only trusted partners have access and that they’re using it appropriately.

• Conduct a formal review at least once a year to confirm which vendors have access to PHI, the scope of that access, and whether it’s still necessary.
• Remove access for any vendors you no longer work with or whose services have changed.

Implementation Guidance for SaaS & HealthTech

Understanding HIPAA rules is one thing – but putting them into practice in a real SaaS or HealthTech environment is where many companies slip up. Modern healthcare products often rely on complex cloud infrastructure, mobile applications, and integrations with multiple vendors and devices. 

Actionable guidance for turning HIPAA requirements into reality. From building a compliant cloud architecture on AWS, GCP, or Azure, to managing the shared responsibility model, to securing mobile apps and monitoring who accesses PHI – you’ll find clear steps to help your engineering, DevOps, and compliance teams stay aligned.

What a HIPAA-compliant cloud setup looks like (AWS/GCP/Azure)

Most SaaS and HealthTech solutions rely on major cloud providers. The good news is AWS, GCP, and Azure all offer HIPAA-eligible services – but simply choosing the right services isn’t enough.

• Sign a BAA: Cloud providers will sign a BAA covering specific HIPAA-eligible services. Make sure yours does – and use only the covered services for PHI workloads.
• Isolate PHI workloads: Use separate, secure VPCs, storage buckets, and databases for PHI.
• Encrypt everything: Data should be encrypted at rest and in transit, using strong encryption protocols.

Shared responsibility model for infra vs app-layer compliance

A common pitfall is assuming your cloud provider handles HIPAA compliance end-to-end. In reality, responsibility is shared – the provider secures the infrastructure, but you must secure your own application and data flows.

• Understand boundaries: The cloud provider handles physical security, network infrastructure, and many core services – but you control how your app stores, processes, and shares PHI.
• Secure your code: Implement strong app-layer security: input validation, secure authentication, role-based access, and data minimization.
• Document responsibilities: Clearly define who owns which controls, internally and with vendors.

Handling mobile apps and HIPAA (user auth, device-level risk)

Mobile apps are central to modern healthcare – from patient portals to remote monitoring tools – but they pose unique risks. Lost devices, weak authentication, or unsecured storage can easily lead to breaches.

• Strong user authentication: Require secure login methods – ideally with multi-factor authentication for both patients and providers.
• Encrypt local storage: If PHI must be stored on a device, encrypt it and limit how long it stays cached.
• Remote wipe: Where possible, enable the ability to remotely wipe sensitive app data if a device is lost or stolen.

Monitoring access to PHI via logs and alerting tools

HIPAA requires you to know who’s accessing PHI – and to detect unauthorized or unusual behavior quickly. Continuous monitoring and alerting are your front line for catching issues before they turn into major breaches.

• Enable detailed audit logs: Track access at every layer – infrastructure, database, and application.
• Centralize logs: Aggregate logs in a secure SIEM (Security Information and Event Management) or log management tool.
• Define alerts: Set up real-time alerts for suspicious activities like repeated failed logins, unusual file downloads, or access from unexpected locations.

Reducing surface area: Minimize PHI processing where possible

One of the most effective ways to manage PHI risk is to limit how much you collect, process, and store in the first place. The less data you hold, the smaller your exposure if something goes wrong.

• Limit collection: Only collect PHI that’s absolutely necessary for delivering your service.
• De-identify data: Where possible, use de-identified or aggregated data for analytics and research.
• Purge old data: Set retention schedules for PHI and delete it securely when it’s no longer needed.

Staying Compliant Over Time

Achieving HIPAA compliance is a big milestone – but keeping it is where many organizations stumble. Regulations evolve, new threats emerge, and your operations, vendors, and technology stack constantly change. For SaaS and HealthTech companies, staying compliant means building routines, clear accountability, and a culture where protecting patient data is an ongoing practice – not a once-a-year checkbox.

Regular risk reviews, up-to-date training, centralized evidence collection, and readiness for audits all help keep your HIPAA safeguards effective and defensible year after year.

Schedule periodic HIPAA risk assessments

HIPAA’s Security Rule requires covered entities and business associates to regularly assess risks to PHI. A risk assessment helps you identify gaps, adapt to new threats, and demonstrate due diligence if an incident occurs.

• Perform a comprehensive risk assessment at least annually and more often if you launch new products, adopt new technologies, or undergo major operational changes.
• Document your findings and prioritize remediation plans with clear timelines and owners.
• Track progress on risk mitigation and follow up on high-risk areas until resolved.

Review policies quarterly and after incidents

HIPAA policies and procedures should be living documents, not static PDFs sitting on a shared drive. New threats, operational shifts, and lessons learned from incidents should all trigger updates.

• Schedule formal policy reviews at least once per quarter.
• Revise procedures immediately after any security incident, breach, or audit finding.
• Communicate changes to your workforce and update training materials so everyone stays aligned.

Employee training and certification refreshers

People make or break compliance. Even the best policies won’t work if your workforce forgets how to apply them. Ongoing training keeps security top-of-mind and reduces the risk of accidental PHI exposure.

• Deliver HIPAA training for all new hires before they access PHI.
• Run annual refresher courses for all employees, contractors, and any partners with access.
• Tailor advanced or role-specific training for staff who handle PHI daily – like developers, support teams, or compliance leads.

Keep audit logs and evidence collection centralized

Your policies and risk assessments don’t mean much if you can’t prove you’re following them. Centralized, organized evidence shows regulators and partners that you’re doing what you say you do.

• Store audit logs, training records, access reports, incident reports, and BAAs in a secure, centralized repository.
• Use tools that help automate evidence collection for easier audits and internal reviews.
• Back up your compliance records regularly and secure them against unauthorized changes.

Be prepared for OCR audits or investigations

The Office for Civil Rights (OCR) enforces HIPAA – and can audit any covered entity or business associate at any time. Preparation is your best defense if you’re selected for an audit or investigated after a breach.

• Designate a HIPAA Privacy and Security Officer to lead your response if the OCR contacts you.
• Keep a documented compliance program that includes all risk assessments, policies, logs, training records, and vendor BAAs.
• Run internal mock audits so you know where your gaps are and how to respond under pressure.

Conclusion

HIPAA is not just a legal checkbox, it’s how you prove to patients, partners, and regulators that you take data privacy and security seriously. The steps outlined in this checklist help you turn compliance from a one-time task into a continuous practice built into your technology, processes, and team culture.

Start early, assign clear ownership, and automate what you can but remember that human oversight and regular reviews are just as critical for staying compliant over time.

If you need help strengthening your HIPAA security posture, whether it’s conducting a risk assessment, testing your defenses, or ensuring your systems are secure by design, SecureLayer7 is here to help. Our experts can support you with tailored security assessments, penetration testing, and ongoing compliance services to keep your patient data safe and your organization audit-ready. Protect your PHI, earn trust, and stay compliant, connect with SecureLayer7 today.

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