Overview

Tax audit appeals are a critical safety valve in the U.S. tax system: they give taxpayers an independent review of audit adjustments before collection or court action. The Office of Appeals is designed to be neutral and to resolve disputes through negotiation when appropriate (IRS, Office of Appeals: https://www.irs.gov/appeals). In my practice as a CPA, I’ve found that the difference between losing and winning an appeals conference usually comes down to two things: the protest document and the supporting administrative record you prepare.

This article explains the timeline, what to include in a written protest, how to organize your exhibits, what to expect in an appeals conference, and practical tips to improve results. It also links to related FinHelp articles for step‑by‑step prep and representation: see our guides on What to Expect in an IRS Appeals Conference and Using a Power of Attorney (Form 2848) During an Audit or Appeal.

Deadlines and when a formal protest is required

  • If you receive a “30‑day letter” (a Notice of Proposed Adjustment or similar letter giving you appeal rights), you generally have 30 days from the date on the notice to request an Appeals review or to file a written protest (IRS, “Your Appeal Rights”).
  • A formal written protest is required when the total amount of the proposed deficiency (tax, penalties, and interest) exceeds $25,000 for any one tax period. For smaller cases, a signed statement explaining the grounds for disagreement and a request for an Appeals conference may be sufficient.
  • If you receive a Statutory Notice of Deficiency (a “90‑day letter”), your route to contesting the deficiency is generally to petition U.S. Tax Court within 90 days (150 days if the notice was mailed to a person outside the United States) rather than the Office of Appeals. Do not miss these deadlines — late protests can limit options.

(Authoritative source: IRS Office of Appeals pages and the appeal rights language provided with audit notices; see https://www.irs.gov/appeals.)

Step‑by‑step: How to prepare and file a written protest

  1. Read the notice carefully
  • Identify the tax periods, issues, and amounts in dispute.
  • Note the deadline and the address or email where the protest should be sent (the notice will direct you).
  1. Decide who will represent you
  • Taxpayers can represent themselves. However, virtually every time a client brought a qualified tax professional, outcomes improved because complex legal and factual issues were better framed. If you appoint someone, file Form 2848 (Power of Attorney). See our guide: Using a Power of Attorney (Form 2848) During an Audit or Appeal.
  1. Prepare the protest document (if required)
  • Required elements (typical): taxpayer name, current address, taxpayer identification number (SSN or EIN), tax form and periods, a statement that you request an Appeals conference, the facts and law supporting each issue, a computation of proposed changes (if applicable), copies/description of documents to be offered, signature (taxpayer or authorized representative), and a daytime phone number.
  • Be concise. Focus on the dispositive facts and the legal basis for each position (statute, regulation, case law if relevant).
  1. Attach supporting exhibits
  • Include only relevant evidence (receipts, invoices, bank statements, canceled checks, contracts, expert reports). Label exhibits and reference them in the protest.
  • Create an indexed exhibit binder or a PDF with a clickable table of contents for faster Appeals review.
  1. Submit the protest
  • Send the protest to the address on the notice or follow the IRS instructions. Keep delivery proof (certified mail, tracked courier, or documented electronic submission).
  1. Confirm receipt and prepare your administrative file
  • Save all correspondence, emails, and administrative contacts. Prepare a succinct appeals brief and an exhibit index to email to the Appeals officer when requested.

What happens next: the appeals conference process

  • Appeals assigns an Appeals Officer who is independent from the audit team. The officer will review the administrative file and may request additional documents.
  • Conferences can be in‑person, by phone, or virtual; the format depends on location, the complexity of issues, and current IRS practices.
  • Appeals focuses on the hazards of litigation — whether the IRS would likely prevail in Tax Court. Cases are resolved by negotiation and settlement when it’s reasonable for both sides.
  • Typical timeline: you can usually expect an initial contact within 30–90 days after filing a protest, but the timeline varies with caseload and case complexity.

For a focused walkthrough of the conference itself, FinHelp’s article What to Expect in an IRS Appeals Conference outlines typical questioning, settlement negotiation strategies, and common pitfalls.

Practical tips for the appeals conference

  • Lead with the strongest facts: open with a 1‑page executive summary that states the relief you want and the top 2–3 reasons the adjustment is incorrect.
  • Use an issues matrix: for each issue list (a) IRS position, (b) taxpayer facts and evidence, (c) legal support, (d) settlement proposal.
  • Avoid emotional language and argument by innuendo. Appeals is an administrative review — crisp factual and legal presentations carry weight.
  • Discuss penalties separately: penalties are treated as distinct issues and may require different evidence (reasonable cause, substantiation, or administrative waiver).
  • Be ready to make a settlement offer: a partial concession with supporting rationale often leads to better outcomes than an all‑or‑nothing stance.

Common mistakes to avoid

  • Waiting until the last minute to gather exhibits — this leads to missed evidence and weak proofs.
  • Submitting voluminous but unindexed documents — Appeals officers appreciate organized, indexed exhibits.
  • Failing to request a conference or missing the 30‑day deadline stated on the notice — this can forfeit administrative appeal rights.
  • Ignoring the hazards‑of‑litigation standard — Appeals settles cases based on risk, not only on who is strictly right.

When to escalate or choose another forum

  • If Appeals and the taxpayer can’t reach an agreement, options include: litigation in U.S. Tax Court (if you received a 90‑day deficiency notice), U.S. District Court, or the U.S. Court of Federal Claims, depending on your procedural posture.
  • Consider litigation if you have a strong legal argument and prefer a public precedent or jury trial (District Court) over negotiation.
  • See our related glossary: Tax Audits and Appeals — When to Take Your Case to Tax Court.

Sample outline for a concise written protest

  1. Cover page: taxpayer name, address, TIN, tax periods, and contested amounts.
  2. Statement of request: “This is a written protest requesting an Appeals conference for the issues listed below.”
  3. Issue list with short statement for each.
  4. Factual summary (chronological, 1–2 paragraphs per issue).
  5. Legal argument (citations to code, regs, or precedent where applicable).
  6. Computation or schedule showing taxpayer’s numbers vs IRS numbers.
  7. Exhibit index and copies.
  8. Signature and date.

Costs and representation considerations

  • Appeals conferences themselves are administrative and do not require fees beyond your professional representation costs.
  • Hiring a CPA or tax attorney increases the cost, but in many cases the professional’s ability to frame issues and spot settlement points offsets fees through lower tax, penalties, or interest.

Final checklist before submitting your protest

  • [ ] Notice read and deadline confirmed
  • [ ] Decide on representation; file Form 2848 if needed
  • [ ] Draft concise written protest with required elements
  • [ ] Organize and index exhibits; create an executive summary
  • [ ] Send by tracked/verified method and retain proof
  • [ ] Prepare a short oral presentation and settlement matrix for the conference

Professional disclaimer

This article is educational and based on general IRS procedures current as of 2025. It is not legal or tax advice for your specific situation. For case‑specific guidance, consult a qualified CPA, enrolled agent, or tax attorney.

Authoritative sources and further reading

  • IRS, Office of Appeals: https://www.irs.gov/appeals
  • IRS notice language: “Your Appeal Rights and How to Prepare a Protest If You Don’t Agree” (included with most audit notices)

Internal FinHelp guides referenced above:

If you want, I can create a downloadable protest template and an exhibits checklist tailored to individual returns (personal or business) to help you file a complete administrative appeal package.