The HIPAA Documentation Requirement: What to Keep, Where, and for How Long (45 CFR 164.316)

Executive Summary

HIPAA compliance doesn’t end with implementing safeguards, it requires clear, accessible, and auditable documentation of your policies, procedures, assessments, and actions. Section 164.316 of the HIPAA Security Rule mandates that covered entities and business associates maintain written documentation of their security policies and related activities for at least six years. For small practices, failure to maintain this documentation can result in penalties even if safeguards are in place. This guide outlines what needs to be documented, how to store it, and for how long, offering a practical roadmap for HIPAA compliance that stands up to audits and investigations.

Introduction

When the Office for Civil Rights (OCR) audits or investigates a small medical practice for HIPAA compliance, one of the first requests is for documentation. It’s not enough to say your practice trains staff, performs risk analyses, or has policies in place—you must have written, dated records to prove it.

The HIPAA Security Rule’s § 164.316 establishes the documentation standard for all security policies and procedures, including those related to ePHI protection. For many small healthcare providers and business associates, this rule is overlooked until it's too late.

This guide is designed to help small practices understand their obligations under § 164.316, what needs to be documented, where to keep it, and for how long.

What § 164.316 Requires

The regulation at 45 CFR § 164.316 states:

“Implement reasonable and appropriate policies and procedures to comply with the standards, implementation specifications, or other requirements of this subpart... Maintain the policies and procedures... in written (which may be electronic) form... and retain them for six years from the date of creation or the date when it last was in effect, whichever is later.”

The key requirements are:

• Written documentation of HIPAA policies and procedures
• Retention of documentation for at least six years
• Availability of documentation to those responsible for implementation
• Periodic review and updates as needed in response to environmental or operational changes

This rule supports other standards under HIPAA, such as those governing access controls, training, risk analysis, audit logs, and breach response.

Why Documentation Matters

• You cannot prove HIPAA compliance during an audit
• You increase liability in the event of a data breach
• OCR may issue fines even if you had protections in place because you can’t prove them
• Business associates and insurers may reject claims or breach coverage due to missing records

Documentation provides a legal and operational foundation for your privacy and security program.

What You Must Document Under § 164.316

Here’s a list of documents small practices are expected to maintain to meet HIPAA’s documentation requirement:

• Security Policies and Procedures – Written policies covering HIPAA Security Rule standards, admin/physical/technical safeguards, access, passwords, remote protocols, etc.
• Risk Analysis and Management Plans – Risk analysis reports, risk mitigation documentation.
• Security Incident Response – Response policy, logs, breach records, OCR communications.
• Workforce Security and Training – Training logs, signed agreements, access records, disciplinary actions.
• Evaluation and Review Activities – Annual technical/nontechnical evaluations, documentation of operational changes.
• Business Associate Agreements (BAAs) – Signed agreements, amendments, and BAA logs.
• Audit Controls and System Activity Review – Monitoring logs, access reports, audit trails.
• Device and Media Controls – Tracking, disposal, re-use logs for PHI devices/media.

Where and How to Store HIPAA Documentation

• Written or electronic form, but must be easily retrievable during an audit or investigation
• Backed up and secured from loss or unauthorized access
• Controlled for version history (track changes over time)

Recommended Storage Options for Small Practices

Use naming conventions and folders to organize by document type and ensure access is restricted to those who need it.

How Long Must You Keep Documentation?

HIPAA requires retention for at least six years from:

• The date of creation, or
• The date it was last in effect, whichever is later

Some examples:

Case Study: HIPAA Fine for Missing Documentation

A small dermatology clinic experienced a ransomware attack that affected their patient scheduling and billing systems. When the OCR investigated the breach, the clinic asserted that it had strong firewalls, antivirus software, and staff training in place.

However, the clinic could not provide any written risk assessments, incident response plans, or training logs.

Despite the fact that technical safeguards were present, the OCR determined the clinic to be non-compliant with the documentation standard under § 164.316.

The clinic entered a resolution agreement that required:

• Immediate documentation of all security activities
• Monthly reporting to OCR
• Third-party oversight for one year

Lesson learned: If it’s not written down, it doesn’t count, even if you did everything right.

Best Practices for Documentation Compliance

1. Assign a Documentation Coordinator – Designate someone to organize and maintain HIPAA documentation (office manager, compliance officer, or external consultant).
2. Maintain a Master Index – Central log with document type, date, file location, and responsible person.
3. Review and Update Annually – Set reminders to review, update, and archive documents yearly.
4. Use Templates and Checklists – Use HHS, NIST, or professional association templates for consistency.
5. Audit Yourself Before OCR Does – Annual internal documentation review; fix gaps proactively.

HIPAA Documentation Compliance Checklist

Common Pitfalls in HIPAA Documentation (§ 164.316)

Many small practices make mistakes that jeopardize HIPAA compliance. These include failing to update policies regularly, using generic templates that don’t match actual operations, lacking proof of completed actions like training or risk assessments, storing documents in a disorganized way, ignoring the six-year retention rule, neglecting to have up-to-date Business Associate Agreements (BAAs), and not assigning a clear person responsible for documentation.

To avoid these pitfalls: review policies annually, customize documentation to your real workflows, keep detailed records of all activities, centralize and organize your files securely, follow retention schedules, maintain current BAAs, and appoint a responsible person with authority to manage all HIPAA documentation. This not only ensures compliance but also protects your practice during audits.

Regulatory References and Tools

• 45 CFR § 164.316 – HIPAA Documentation Requirements
• HHS HIPAA Security Rule Guidance
• NIST SP 800-66 – HIPAA Implementation Guide
• OCR Audit Protocol

Final Takeaways and Recommendations

If your HIPAA program isn’t documented, it might as well not exist. Section 164.316 of the Security Rule requires that every policy, assessment, and safeguard related to PHI be written, retained, and accessible for six years. This includes not just what you plan to do but what you actually did.

For small practices, the key to compliance is organization and consistency. Assign responsibility, use templates, review documents annually, and store everything in a secure location. It may seem tedious, but your documentation could be the deciding factor in avoiding fines during an audit or defending your practice after a breach.