6-Step HIPAA Audit Checklist for Healthcare Organizations

Failing a HIPAA audit carries heavy financial risks and, more importantly, damages the trust that patients and partners place in the entire healthcare system.

In this article, we’re preparing your organization by going over:

• What a HIPAA audit is
• The best HIPAA audit checklist for complete compliance
• Common HIPAA violations
• How email archiving supports HIPAA compliance

Key Takeaways

Just looking for a quick HIPAA audit checklist?

Here are the key steps (more info later in this guide):

• Assess your organization: Conduct a security risk assessment and check for hidden security gaps in your organization.
• Set administrative policies: Set up protocols and written policies meant to safeguard protected health information (PHI).
• Secure physical environment: Create strategies to protect the physical environment where protected health information (PHI) is stored.
• Take technical measures: Use the latest security technologies and transmission protocols to prevent unauthorized access.
• Implement organizational requirements: Maintain Business Associate Agreements (BAAs) and ensure third parties meet HIPAA requirements.
• Create an incident response plan: Establish protocols for patient information breaches, including detection, response, notification, and mitigation procedures.

What Is a HIPAA Audit?

A HIPAA compliance audit evaluates how covered entities and Business Associates (BAs) comply with the HIPAA Privacy Rule, Security Rule, and Breach Notification Rule when handling PHI.

Audits focus on whether an organization has:

• Implemented required safeguards
• Documented policies and procedures
• Evidence that controls are operating as intended

HIPAA audits generally fall into two categories: external audits conducted by regulators and internal compliance reviews performed by the organization.

External HIPAA audit

The U.S. Department of Health and Human Services Office for Civil Rights (OCR) administers the federal HIPAA audit program. These audits assess compliance with HIPAA audit requirements across selected covered entities and Business Associates.

OCR audits are not routine or annual inspections. OCR periodically initiates audit cycles and selects a limited number of organizations for review. The latest 2024–2025 audit initiative focused primarily on Security Rule compliance, with particular attention to cybersecurity risks such as hacking and ransomware. The previous major audit cycle occurred in 2016–2017.

During an external HIPAA audit, OCR evaluates whether required safeguards are:

• Properly implemented
• Appropriately documented
• Consistent with HIPAA regulations and guidance

Even if your organization is never selected for a formal OCR audit, OCR may initiate a compliance review or investigation at any time in response to:

• Reported data breaches
• Patient complaints
• Patterns of non-compliance identified through enforcement activity

Internal HIPAA audit

HIPAA does not mandate a formally named audit on a fixed schedule. However, it requires covered entities and Business Associates to regularly evaluate their compliance through ongoing risk analysis, monitoring, and review.

Internal HIPAA audits, often referred to as self-assessments, help organizations verify that their safeguards align with HIPAA audit requirements and OCR expectations. These reviews typically assess:

• Administrative, physical, and technical safeguards
• Workforce access and training
• System activity, audit logs, and access reports
• Incident response and breach documentation

Under the HIPAA Security Rule, organizations must periodically review information system activity, including audit logs and access reports. In January 2025, OCR proposed updates to the Security Rule that would further formalize these obligations, potentially requiring more structured and documented compliance evaluations. These updates are proposed and not yet final, but they reflect OCR’s enforcement direction.

As a best practice, many organizations conduct a comprehensive internal HIPAA audit at least annually, with more frequent reviews for high-risk systems, operational changes, or following a security incident.

What happens if you fail a HIPAA compliance audit?

Failing to pass a HIPAA audit, either external or internal, brings with it a set of consequences depending on the severity of the violation and the organization’s response to the findings. These consequences can include penalties and fines, increased oversight, damage to reputation, or mandated corrective action plans.

The best way to stay ahead is to use a HIPAA checklist to fix vulnerabilities now, rather than wait for a security breach or an OCR audit to force a high-stakes cleanup.

6-Step HIPAA Audit Checklist

Complying with HIPAA isn’t an easy job for any healthcare organization, and audits just make it harder, but following the right guidelines will set you up for full compliance.

Use this HIPAA audit checklist and take the key steps for your organization to prepare for a HIPAA audit:

Assess your organization

Conduct a HIPAA Security Risk Analysis and identify security gaps in your organization

• Thoroughly review all HIPAA rules and regulations, and how you are handling them.
• Analyze previous data breaches and HIPAA non-compliance situations.
• Document all deficiencies you found.

Implement administrative safeguards

Set up protocols and policies meant to safeguard protected health information (PHI).

• Develop and implement necessary security protocols and procedures uncovered after the assessment.
• Designate a security officer to oversee and implement security measures.
• Document the new security measures and create employee training plans.
• Provide employees with security awareness training.
• Implement access limitations to patient information based on employee roles.

Implement physical safeguards

Create strategies for guarding the physical environment where the protected health information (PHI) is stored.

• Develop and implement security policies to control physical access to physical storage facilities.
• Implement security measure standards like access cards and personnel checks.
• Secure employee workstations from unauthorized access.
• Implement measures for the disposal of electronic devices.
• Apply encryption or equivalent compensating controls for portable devices containing PHI, where reasonable and appropriate.

Implement technical safeguards

Use the latest security technologies and transmission protocols to prevent unauthorized access.

• Implement user identification for system access with strong authentication methods.
• Establish regular audit log reviews and processes.
• Ensure proper measures to ensure your data’s integrity.
• Utilize industry encryption standards to protect your patients’ data.

Implement organizational requirements

Manage all of your organization’s partnerships, agreements, and obligations.

• Identify your vendors and business associates.
• Obtain and maintain satisfactory assurances through Business Associate Agreements (BAAs), and take appropriate action if a business associate is found to be non-compliant.
• Establish or re-establish agreements with business associates handling patient information.
• Keep up-to-date documentation of security policies and procedures.

Create an incident response plan

This step is all about setting up protocols in the case of patient information breaches.

• Develop a clear breach response plan according to your new processes and assessments.
• Ensure all employees understand the plan.
• Conduct breach simulations or tabletop exercises as a best practice to test response readiness.
• Document the simulations and real incidents for further improvements.

Following this HIPAA audit checklist helps position your organization to meet HIPAA audit requirements and reduce compliance risk.

It’s recommended to regularly review and update your HIPAA compliance strategy to comply with new regulations and address any issues.

Protect your healthcare organization from compliance fines and penalties.

Explore secure, next-generation data archiving solutions from Jatheon.

Types of HIPAA Violations that Can Trigger an Early HIPAA Audit

HIPAA audits are not routine inspections of every healthcare organization. However, certain HIPAA violations can raise red flags and prompt the Office for Civil Rights (OCR) to initiate an investigation or compliance review.

These enforcement actions often require organizations to produce the same documentation reviewed during a formal HIPAA audit.

The most common HIPAA violations that frequently lead to OCR scrutiny include:

• Unauthorized access to PHI — If an unauthorized person gained access to confidential patient information, this can alert authorities to conduct a thorough HIPAA audit due to further security risks.
• Lack of patient authorization — Sharing patient information without proper authorization can prompt the patient to file a complaint, which can trigger an investigation.
• Failure to notify patients of a breach — HIPAA requires covered entities to notify affected individuals, regulators, and, in some cases, the media within specific timeframes. Missed or delayed notifications are a frequent enforcement finding.
• Improper disposal of PHI — An instance of someone finding a patient’s file improperly disposed of (not shredded) can prompt a full HIPAA audit.

Addressing these risk areas is essential to meeting HIPAA audit requirements and reducing the likelihood of enforcement actions.

Using a structured HIPAA audit checklist helps organizations identify these gaps early and demonstrate compliance if OCR initiates an investigation or audit.

How Email Archiving Helps You Comply with HIPAA

Most healthcare information, patient scheduling, and contracts with BAs get sent over email, so it’s one of the biggest threats to your HIPAA compliance.

To reduce compliance risk and support audit readiness, your email communications need to be archived for optimal data security.

HIPAA requires certain compliance documentation to be retained for six years. Email archiving can help preserve emails that qualify as required records.

To make it as easy as possible for your HIPAA compliance, email archiving solutions have many features that help you stay secure.

These features include:

• Automated information capture — The archive captures emails from major platforms and stores messages with full context (body, headers, recipients, timestamps, and attachments). If you also archive other channels (SMS, chat, social), those records can be retained in the same system, including edits and deletions where supported.
• Deployment flexibility (cloud, on-prem, virtual) — For healthcare IT teams, deployment affects security architecture, access boundaries, and vendor oversight. Jatheon supports AWS-based, on-premises, and virtual deployment options, so you can align the archive with internal policies and risk decisions.
• Data security — Encryption and 2FA/MFA options help reduce unauthorized access risk and support HIPAA technical safeguards. HIPAA treats encryption as an addressable specification, so it should be tied back to your risk analysis and documented decisions.
• Data preservation — Retention policies can be configured to align with HIPAA’s six-year documentation retention requirement. HIPAA requires retaining certain compliance documentation for six years, while message retention is often driven by organizational policy, state rules, and legal considerations.
• Data integrity — A HIPAA audit requires you to prove your communications weren’t tampered with or deleted. Email archives allow you to store the original instance of an email in a WORM format and come with message integrity verification features.
• Access control — Your compliance officers can easily assign roles in your organization and give only the necessary permissions to each employee.
• Search, review, and export tools — Advanced search and export capabilities help teams locate and produce relevant messages quickly for audits, investigations, and legal matters. Redaction tools can further help limit unnecessary exposure of sensitive information during review and production.
• Audit trails and supervision — Email archiving solutions allow you to go through every action taken inside your archive, helping you respond to HIPAA audit requests and improve your HIPAA compliance through analysis.

Email archiving can play an important role in supporting HIPAA compliance and audit readiness.

Beyond it, modern healthcare organizations rely on a variety of digital channels to maintain operations and deliver care.

From telehealth sessions on Zoom, Meet, or Teams to quick coordination via messaging apps, including WhatsApp, SMS, or iMessage, PHI now lives across multiple platforms. Such fragmentation creates compliance gaps that are often overlooked. To address this, Jatheon offers a unified archiving approach that captures communications across all these channels in a single, secure, searchable archive. This means that no matter where a conversation happens, it is protected and easily retrievable.

Summary of the Main Points

• A HIPAA audit evaluates how covered entities and Business Associates comply with the Privacy Rule, Security Rule, and Breach Notification Rule.
• The Office for Civil Rights (OCR) runs the only federal HIPAA audit program and conducts audits periodically, not on a routine or annual basis.
• HIPAA does not require audits on a fixed schedule, but it does require ongoing risk analysis, monitoring, and compliance review.
• A structured HIPAA audit checklist helps organizations assess administrative, physical, technical, and organizational safeguards.
• Common HIPAA violations, such as unauthorized PHI access, improper disclosures, missed breach notifications, and improper disposal, often trigger OCR investigations or compliance reviews.
• Email archiving is not mandated by HIPAA, but it can support compliance by preserving required documentation, maintaining data integrity, and improving audit readiness.
• Proactive internal reviews and documented safeguards reduce compliance risk and help organizations respond effectively to OCR audits or investigations.

FAQ

How often are HIPAA audits done?

Covered entities and Business Associates must regularly evaluate their compliance through risk analysis, monitoring, and review of safeguards. The frequency of internal reviews depends on factors such as operational changes, new technology, or security incidents.

Who can perform a HIPAA audit?

External HIPAA audits are conducted by the U.S. Department of Health and Human Services Office for Civil Rights (OCR) as part of its federal audit program or enforcement activity. Internal HIPAA audits or assessments may be performed by a designated compliance officer, internal audit team, or third-party compliance firm to evaluate alignment with HIPAA requirements and OCR guidance.

How much does a HIPAA audit cost?

OCR-conducted HIPAA audits do not have a direct fee, but responding to an audit can require significant internal time and resources. The cost of an internal HIPAA audit varies widely depending on scope, organization size, and whether a third-party firm is used. Costs may range from a few thousand dollars to significantly more for comprehensive enterprise assessments.

How long does it take to complete a HIPAA audit?

The length of a HIPAA audit varies depending on scope and complexity. OCR audits often begin with a document request, followed by a review period and written findings. When selected by OCR, organizations are typically given a limited timeframe to submit requested documentation and respond to draft findings. The full process can take several weeks to several months, depending on the audit or investigation.

How many HIPAA audit programs are there?

There is one federal HIPAA audit program, run by the U.S. Department of Health and Human Services Office for Civil Rights (OCR). OCR conducts periodic audit cycles under this program. Internal or third-party HIPAA audits are voluntary compliance reviews, not separate audit programs.

About the Author

Bojana Krstic

Bojana Krstic is the Marketing Director at Jatheon, where she leads strategic initiatives and creates content on data archiving, ediscovery, and compliance. When AFK, you’ll find her in the forest, discovering new music, or exploring the Adriatic.