Are Your Employee Files in Order?

What to Keep, What to Separate, and How Long to Store It All.
employee files in order

Managing employee records isn’t the most glamorous part of HR, but it’s a critical one, especially in healthcare practices where compliance, confidentiality, and clarity are key. We consulted with Debbie Strawser of Reserve Squad to find out what should be included in employee files, what belongs elsewhere, who can access what, and how long you need to retain each type of record.

What Belongs

An employee file should tell the full story of someone’s employment from application to exit. Here are the core components:

  • Hiring Documents: Application, resume, offer letter, employment agreement, background check results, and handbook acknowledgements.
  • Compensation Records: Starting pay, any merit increases or adjustments, and promotions that impact
  • Performance and Other Feedback: Appraisals, disciplinary notes, letters of praise, and relevant attendance documentation. Keep good and bad
  • Licenses and Certifications: Keep current copies and verify independently (especially for roles like nurses or other credentialed staff). A tickler system can help track
  • Training Records: Especially HIPAA and compliance-related You can also store these in a master training file as long as they’re accessible.
  • Payroll-Related Info: Garnishments, employment verifications, and emergency contact information.
  • Separation Documents: Resignation letters, termination paperwork, unemployment claims, and severance agreements.

What to Keep Separate

Certain information should never be stored in the general employee file:

  • Medical and Leave Info: FMLA paperwork, accommodation requests, doctor’s notes, workers’ comp claims.
  • Benefit Enrollment Forms: Especially those that include Social Security numbers, dates of birth, or health conditions.
  • Drug Testing Results: Store separately and securely.
  • Forms I-9: Best practice is to keep these in a separate binder or file, organized, and up to date.
  • Investigation Files: If no action is taken following an internal investigation (e.g., harassment claims), store those notes apart from the general file.

Paper vs. Electronic Files

Electronic HR systems can reduce paper clutter as long as they’re secure and easily searchable. If you’re working with physical files, invest in divided folders to organize sections like hiring, performance, pay, and separation. Store all files in a locked cabinet, in a secure space, with limited access. Another important consideration is disaster recovery scenarios where physical copies of records can be destroyed or are inaccessible for long periods of time.

Who Gets Access?

Access to employee files should be limited. Managers may need to see resumes or performance reviews but not benefit or medical information. If an employee requests to review their file, schedule a time, and only share documents they’re entitled to see, such as anything they’ve signed.

Never release employment or payroll information to outside parties (e.g., for loans or job references) without a signed release from the employee.

Law enforcement/government requests – dates of employment and position are fine. Check with legal counsel if more information is required.

How Long Should You Keep It?

Here’s a quick guide to retention:

  • Forms I-9: 3 years after hire or 1 year after termination, whichever is later.
  • Recruiting Documents: 1 year after hire or when the search is ended, unless applicants are challenging decision, then keep longer.
  • Background Checks: At least 5 years (this can vary by industry, so check your requirements).
  • Disciplinary Records: Best to retain for the duration of employment.
  • Benefit & ERISA Docs: At least 6 years post-employment but often longer for retirement plans.
  • FMLA Records: 3 years after the leave ends.
  • Payroll Records: 5 years minimum

When it’s time to dispose of records, do so securely. Shredding is your safest bet or work with a professional disposal firm.

Need Help or Have Questions?

If you’re unsure how to set up or manage your employee files or have any other HR needs, reach out to our team at Scroggins. We’ve helped medical practices navigate these and many other challenges for over 80 years and are happy to help.

Debbie Strawser, SPHR, SHRM-SCP

Continue Reading

Smiling nurse standing in front of a medical team

2025 Brings Changes to 401(k) Eligibility for Part-Time Employees

Learn why enrolling long-term part-time employees in your company retirement plan is now required after just two years (500+ hours). Discover compliance requirements, benefits, and 2025 deferral rates.
Wooden blocks with the words Tax Relief stamped on them next to a calculator

Federal Disaster Tax Relief Act Expands Support for Disaster-Related Losses

The Federal Disaster Tax Relief Act of 2023 offers expanded tax benefits for disaster victims. Learn about simplified deductions, extended deadlines, and special credits for losses from hurricanes, wildfires, and other federally declared disasters since 2019.
Doctor ripping open shirt to show superhero costume

Your Independence is a Super Power

Discover how independent medical practices compete with large healthcare systems by offering physicians freedom, flexibility, and control. Learn why workplace culture and autonomy are powerful tools for attracting top medical talent.
Busy reception desk and waiting room

The Power of Patient Experience: Why Every Element Matters

Discover how every staff interaction shapes patient experience beyond clinical care. Learn practical strategies for healthcare practices to improve satisfaction, from front desk engagement to technology integration, creating a culture of care that benefits patients and staff alike.
An illustration showing rows of people with one smiling individual highlighted in red

The Right People for the Right Seats

How to use assessments to find the best candidates for your open roles.

There’s a Path Back for Doctors to Return to Independent Practice

Discover how physicians are successfully returning to independent practice with better tools, support services, and evolving compensation models making the transition more feasible than ever.

Cyber Readiness for Small Practices: Practical Steps That Make All the Difference

Here’s what providers need to know about today’s threat landscape, and what you can do to protect your practice, your revenue, and your reputation.
A Family Firm with an Independent Streak

A Family Firm with an Independent Streak

Scroggins has made it our mission to help doctors stay in control of their work and their future.

Finding Freedom in Independent Practice

Dr. Petit’s Journey to Petit Dermatology

Strategies for practices to maintain their autonomy

After decades of consolidation, private medical practices face a new kind of challenge
retirement planning 2026

Retirement Planning Opportunities and Key Updates for 2026

resume-small-practice

Small Practice, Big Benefits: How Independent Medical Practices Can Compete for Top Talent

Helping our clients
thrive since 1945.

PROVEN LEGACY

80+ years

Serving clients throughout Ohio, Indiana, and Kentucky since 1945

REGIONAL EXPERIENCE

375+

Medical and dental practices, nonprofits, and private businesses place their trust in us.

CLIENT COMMITMENT

95%

Long-term partnerships with independent medical practices, nonprofits, and privately-held businesses spanning multiple generations.

Schedule a discovery call

Discover how we can help you conquer the endless challenges of managing your organization.