Tax & Compliance

What records do I need to keep for an IRS audit?

Keep tax records for at least 3 years after filing (the general period of limitations), 6 years if you left out income of more than 25 percent of the gross income on the return, 4 years for employment tax records, and asset records until the limitations period ends for the year you dispose of the asset. Fraudulent or unfiled returns have no limit, HIPAA documentation must be kept 6 years, and medical record retention is set by state law.

Reviewed by Stanislav Sukhinin, CFALast reviewed September 30, 2026

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Definition

IRS audit records are the books, receipts, invoices, contracts, and supporting documentation a business is required to maintain to substantiate items on filed tax returns.

The detail

IRS Publication 583 sets the recordkeeping baseline. The general period of limitations is 3 years from the return filing date (a return filed early counts as filed on the due date); this is the minimum retention period for most records. It extends to 6 years if you did not report income that is more than 25 percent of the gross income shown on the return, and to 7 years for a claim for a loss from worthless securities or a bad debt deduction. There is no limit for fraudulent returns or unfiled returns. Employment tax records must be kept for at least 4 years after the tax becomes due or is paid, whichever is later. Keep asset records (equipment, real estate, leasehold improvements) until the period of limitations expires for the year you dispose of the asset, because basis drives depreciation and the gain or loss on sale. For retirement plans, ERISA requires the records behind plan filings to be kept for at least six years after the filing date; keep the plan documents themselves for as long as the plan exists. HIPAA does not set a retention period for medical records; state law does. HIPAA's six-year rule covers the documentation HIPAA itself requires, such as policies and procedures, counted from creation or the date last in effect. Medicare adds its own requirement: a CMS fact sheet tells providers and suppliers that furnish or order Medicare services to keep medical records for 7 years from the date of service. Practical recommendation for medical practices: keep all bank statements, deposit records, payroll registers, AP invoices, fixed asset detail, and tax returns indefinitely in digital form. Storage cost is negligible; reconstructing destroyed records under audit is slow and rarely convincing.

  • The general IRS period of limitations is 3 years after filing; it is 6 years if unreported income is more than 25% of the gross income shown on the return, and there is no limit for a fraudulent or unfiled return.

    Source: IRS Publication 583

  • The HIPAA Privacy Rule does not include medical record retention requirements; state laws generally govern how long medical records are kept.

    Source: HHS: HIPAA FAQ on medical record retention

  • Keep records relating to property until the period of limitations expires for the year in which you dispose of it in a taxable disposition.

    Source: IRS Publication 583

What this means for clinic owners

From Sorso

Digital storage is cheap. Retain all financial records indefinitely. The strongest audit defense is producing original documents on demand; reconstructing them after the fact rarely satisfies an examiner.

Stanislav Sukhinin, CFA

Talk it through

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Related questions

How much does healthcare accounting cost per month?

Sorso's outsourced healthcare accounting starts at $2,000 a month; we know of no survey that publishes a market rate, so other firms' quotes vary with transaction volume, number of locations and how much review you get. The in-house alternative costs more: one accountant at the BLS median wage of $83,680 (May 2025) comes to about $102,600 a year, roughly $8,550 a month, once benefits are added (Sorso estimate).

What tax deductions are available to medical practices?

Medical practices can deduct ordinary business expenses including staff wages, rent, equipment depreciation, supplies, malpractice insurance, CME, retirement plan contributions, and qualified business income (QBI) where eligible.

What is Section 179 for medical equipment?

Section 179 lets medical practices immediately expense up to $2.5M of qualifying equipment placed in service in the tax year (for tax years beginning after Dec 31, 2024, per OBBBA — Public Law 119-21, signed July 4, 2025; $2.56M for tax year 2026 per Rev. Proc. 2025-32), instead of depreciating it over multiple years.

How do I structure a practice for tax efficiency?

A tax-efficient practice structure usually starts with an S corporation election for the clinical practice (held in a PC or PLLC where state law requires one) and a retirement plan sized to the owners' income, with a separate real estate LLC or MSO added for liability, financing or exit reasons. Those extra entities do not preserve the QBI deduction when the same owners hold 50 percent or more of both sides.

What is modifier 25 used for?

Modifier 25 indicates that a significant, separately identifiable Evaluation and Management (E/M) service was performed by the same physician on the same day as a procedure, allowing both to be billed when properly documented.

How do you prepare a medical practice for a Medicare RAC audit?

Preparing for a Medicare Recovery Audit Contractor (RAC) audit comes down to documentation discipline, internal coding audits, and a defined response workflow. The RAC reviews paid claims to identify improper payments, and you have 45 days to respond to medical record requests. Practices that audit their own coding quarterly, retain documentation per CMS rules, and assign a clear point person handle RAC inquiries as routine; practices that do none of those things treat each request as a crisis.

Stanislav Sukhinin, CFA — Founder of Sorso
Stanislav Sukhinin, CFA

Founder of Sorso and a CFA charterholder. Before Sorso, Stan spent 19 years in corporate finance at institutions including UniCredit and Société Générale — managing a $450M loan portfolio and making senior partner at a major mezzanine lender by 29 — then built a fractional CFO firm exclusively for outpatient healthcare clinics.

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