How to Appeal an IRS Audit: From IRC 6213 Notices to Tax Court

Overview

If the IRS proposes adjustments after an examination it will often issue a Notice of Deficiency (a “90‑day letter”) under IRC §6213. You can either request an administrative review through the IRS Office of Appeals or file a petition in U.S. Tax Court. Both routes preserve your dispute rights but follow different procedures, timelines, and evidentiary standards (IRS Pub. 556; U.S. Tax Court: https://www.ustaxcourt.gov/).

Quick steps to appeal

• Read the Notice of Deficiency carefully; note the deadline (90 days; 150 days if abroad). (IRC §6213; see IRS Pub. 556).
• Decide whether to pursue an administrative appeal with the IRS Office of Appeals or file a Tax Court petition.
• Gather and organize documents that directly support each item you contest.
• If pursuing Appeals, submit a clear written protest or request an Appeals conference as the IRS instructs.
• If filing in Tax Court, prepare a petition and pay attention to filing rules and service requirements.

When to use the Office of Appeals vs. Tax Court

• Office of Appeals (administrative): Best when you want a negotiated settlement without litigation. Appeals offers a neutral reviewer and often resolves cases without interest accruing on assessments once a case is under protest. Start here if you want to preserve settlement flexibility (IRS Office of Appeals).

• U.S. Tax Court (judicial): Use when you want an independent, binding court decision and to litigate legal issues. Filing a timely petition in Tax Court prevents immediate assessment and collection of the proposed deficiency for the period provided under §6213.

Key deadlines and timelines

• 90 days from the Notice of Deficiency to file a Tax Court petition (150 days if notice was mailed to someone outside the U.S.). Missing the deadline usually means you lose the Tax Court forum (IRC §6213; IRS Pub. 556).
• Administrative Appeals timelines vary; request an Appeals conference promptly and follow any IRS instructions in the audit report.
• Appeals reviews can take months; Tax Court litigation typically takes longer and may include pretrial discovery and motions.

How to prepare a strong appeal (practical checklist)

1. Read the notice line‑by‑line and list specific items you contest.
2. Gather primary evidence: bank records, invoices, contracts, 1099s, canceled checks, payroll records, and contemporaneous logs.
3. Prepare a concise written protest when required: state facts, legal arguments, the tax years and amounts at issue, and the relief you seek. For smaller dollar issues use the small case (S‑case) procedure if offered.
4. Create an exhibit binder with numbered documents and a table of contents—this speeds review at Appeals (see our guide: Preparing an Audit Binder).
5. Keep communications professional and in writing where possible; summarize oral discussions in follow‑up letters or emails.

Common mistakes to avoid

• Ignoring the notice or missing the 90‑day deadline. Even honest mistakes on dates can forfeit the Tax Court option.
• Sending incomplete documentation or rambling narratives—Appeals reviewers want focused evidence linked to each adjustment.
• Failing to identify the exact legal or factual basis for your disagreement.

What to expect at an Appeals conference

Appeals is less formal than court; the Appeals officer is a neutral adjudicator who seeks a fair resolution. Expect to: exchange documents, explain your position succinctly, and discuss settlement possibilities. In my experience working with tax professionals, presenting a clear, issue‑by‑issue exhibit binder and reasonable settlement ranges increases the chance of a favorable outcome.

If you file in Tax Court

• File a timely petition following the rules at the U.S. Tax Court. Court litigation allows discovery, motions, and a judge’s ruling; it can involve higher costs and longer timelines but provides a definitive legal outcome.
• Consider settlement negotiations even after filing—many Tax Court cases settle before trial.

Practical examples (short)

• Unreported 1099 income: provide bank deposits, client receipts, or corrected 1099s to show income was reported or attributable to loans/gifts.
• Disallowed business expense: supply invoices, contemporaneous mileage logs, and a clear business purpose tied to the deduction.

Resources and authoritative references

• IRS Publication 556, Examination of Returns, Appeals Rights, and Claims for Refund: https://www.irs.gov/pub/irs-pdf/p556.pdf
• IRS Office of Appeals: https://www.irs.gov/appeals
• U.S. Tax Court, How to File a Petition: https://www.ustaxcourt.gov/

Internal resources

• Preparing an Audit Binder: Documents to Organize Before an IRS Audit — https://finhelp.io/glossary/preparing-an-audit-binder-documents-to-organize-before-an-irs-audit/
• How to Appeal an IRS Audit Determination: Steps and Timelines — https://finhelp.io/glossary/how-to-appeal-an-irs-audit-determination-steps-and-timelines/

Professional tips

• Act immediately: start gathering records the day you receive an audit notice.
• Be concise: Appeals reviewers and judges focus on the specific issue—avoid unnecessary background.
• Use experts where needed: CPAs, enrolled agents, and tax attorneys add credibility for complex issues.

FAQs

Q: What if I miss the 90‑day deadline?
A: If you miss the 90‑day deadline to file in Tax Court you typically lose the ability to litigate in Tax Court; you may still pursue administrative remedies or pay and later seek refund litigation, but options and timing differ.

Q: Can I represent myself?
A: Yes, taxpayers may represent themselves in Appeals or Tax Court, but professional representation is often advisable for complex audits.

Disclaimer

This article is educational and does not constitute legal or tax advice. For personalized guidance tailored to your facts and the latest law, consult a qualified tax professional.