Learn · Insurance Appeals

How to appeal an insurance denial for rare disease.

Most first-time denials are overturned on appeal — with the right documentation. Here is exactly how to do it.

Last updated March 2026

To appeal an insurance denial for a rare disease, you need to: identify the exact denial reason in your Explanation of Benefits (EOB), gather peer-reviewed clinical evidence supporting medical necessity, obtain a letter of medical necessity from your doctor, and submit a formal written appeal within your plan's deadline — usually 180 days. Most insurers are required to decide internal appeals within 60 days.

What does an insurance denial actually mean?

A denial letter from your insurer means the plan has decided a treatment, medication, or service is not covered under your current policy. For rare disease patients, denials typically fall into one of four categories: not medically necessary (the most common), experimental or investigational, not covered under your plan, or step therapy not completed.

The denial itself is not a final answer. Under the Affordable Care Act, all health plans sold in the US are required to offer an internal appeals process. Studies consistently show that patients who appeal have a high rate of success — but most patients never appeal at all.

Step 1 — What should I do first when I receive a denial letter?

Your Explanation of Benefits (EOB) contains the specific denial reason code. This is the most important document in the appeal process. The denial reason determines what evidence you need.

Look for: the specific reason for denial (not just "not medically necessary" but the exact policy language used), the deadline to file an appeal, the name and contact information for the appeals department, and any reference to the policy section used to justify the denial.

If the letter doesn't include these details, call the member services number on your insurance card and ask for a written explanation that includes the specific clinical criteria used. You are entitled to this under federal law.

Step 2 — Where do I find my insurer's coverage policy?

Every insurer publishes coverage determination policies — also called medical policies or clinical coverage guidelines — for each treatment category. These are usually available on your insurer's website by searching for the treatment name plus "clinical policy" or "coverage guidelines."

This document is critical because it tells you exactly what criteria your insurer uses to approve the treatment. If your doctor's documentation meets those criteria, your appeal can quote the insurer's own policy language back to them — which is far more persuasive than citing external evidence alone.

Step 3 — What clinical evidence should I include in my appeal?

For rare disease denials, the medical literature is your strongest tool. PubMed is the public database of peer-reviewed medical research and is free to search. Look for systematic reviews and meta-analyses, and clinical practice guidelines from condition-specific organizations such as The Ehlers-Danlos Society, Dysautonomia International, and The Mastocytosis Society.

For rare diseases, case series and expert consensus guidelines are often the best available evidence — this is normal and accepted in appeal decisions. Your appeal should acknowledge the limited evidence base while citing the strongest available support.

Step 4 — What should a letter of medical necessity include?

A letter of medical necessity (LMN) from your treating physician is required for almost every appeal. Ask your doctor to include: your diagnosis and its clinical basis, why the denied treatment is appropriate for your specific presentation, why alternatives are not appropriate for you, the expected outcome of the treatment, and references to peer-reviewed clinical evidence.

A generic "this patient needs this medication" letter will not move the argument. A letter that addresses your insurer's specific denial criteria by name — ideally using the insurer's own policy language — is significantly more effective.

Step 5 — How do I write and submit the appeal letter?

Your appeal letter should open with a clear statement of what you are appealing and what outcome you are requesting. Then address the denial reason directly — don't ignore it or work around it, engage with it point by point.

The structure that works: (1) state the denial you are appealing, including the denial date and reference number, (2) explain why the denial reason does not apply to your case using the insurer's own policy criteria, (3) present your clinical evidence with specific citations, (4) attach the letter of medical necessity and relevant records, (5) state clearly what you are asking for.

Submit via certified mail or through your insurer's secure online portal if available. Keep a copy of everything.

What if the internal appeal is denied?

Under the ACA, you have the right to an external review by an independent review organization (IRO). The IRO's decision is binding on the insurer. Request external review within 60 days of receiving your internal appeal denial.

Other escalation paths: file a complaint with your state insurance commissioner, contact your state's Consumer Assistance Program, or — for employer-sponsored plans — contact the US Department of Labor's Employee Benefits Security Administration (EBSA).

What works specifically for EDS, POTS, and MCAS insurance appeals?

For EDS: physical therapy, IVIG, and pain management medications are commonly denied. Cite clinical practice guidelines from The Ehlers-Danlos Society and published case series on the effectiveness of the specific treatment.

For POTS: beta blockers, fludrocortisone, and midodrine are commonly denied as "not medically necessary." Cite the 2015 Heart Rhythm Society Expert Consensus Statement by Sheldon et al., which established diagnostic criteria and treatment recommendations for POTS, IST, and vasovagal syncope.

For MCAS: mast cell stabilizers and epinephrine auto-injectors are sometimes denied. The Mastocytosis Society's diagnostic and treatment consensus papers are the strongest citations available.

This guide is for informational purposes only and does not constitute legal or medical advice. Insurance appeals involve complex legal and medical questions specific to your plan and condition. Consult your healthcare provider and, for complex disputes, an attorney specializing in insurance law or a certified patient advocate.

About this content

Written by the Atlas Rare team. Last reviewed March 2026. Sources: US Department of Health and Human Services ACA appeals guidance, CMS external review rules, The Ehlers-Danlos Society clinical guidelines, Dysautonomia International, The Mastocytosis Society, Sheldon et al. 2015 Heart Rhythm Society Expert Consensus Statement (Heart Rhythm, Vol. 12, Issue 6). This page is updated when federal regulations or major clinical guidelines change.

Frequently asked questions

Most insurers give you 180 days (6 months) from the date of the denial letter to file an internal appeal. Some plans have shorter windows — 30 to 60 days — so read your denial letter immediately. If you miss the internal appeal deadline, you may still have the right to an external review.

An internal appeal goes back to your insurance company and is reviewed by someone different from the person who made the original denial decision. An external review is conducted by an independent organization not affiliated with your insurer. Under the ACA, you have the right to an external review if your internal appeal is denied.

Your appeal letter should include: the specific denial reason from your EOB, your insurer's own coverage policy language, peer-reviewed clinical evidence supporting medical necessity (PubMed citations), a letter of medical necessity from your treating physician, documentation of failed prior treatments if step therapy was required, and a clear statement of why the denial reason does not apply to your case.

Step therapy (also called fail-first) is when an insurer requires you to try and fail a cheaper treatment before approving the treatment your doctor recommended. To appeal, you need documentation that: (1) you already tried and failed the required treatments, or (2) the required treatments are contraindicated for your specific condition, or (3) your condition is rare enough that the step therapy protocol does not apply. Many states have step therapy exception laws — check your state's requirements.

Yes. A physician-initiated appeal (also called a peer-to-peer review) can be highly effective. Your doctor calls the insurer's medical director directly to discuss the denial. This is separate from the formal written appeal process and can sometimes resolve a denial faster. Ask your doctor's office specifically about requesting a peer-to-peer review.

If your internal appeal is denied, you have the right to request an external review by an independent review organization (IRO) under the ACA. You can also file a complaint with your state insurance commissioner, contact your state's insurance consumer assistance program, or consult a patient advocate. For employer-sponsored plans governed by ERISA, the process differs and an attorney specializing in insurance law may be helpful.

Internal appeals for non-urgent care must be decided within 60 days. Urgent care appeals must be decided within 72 hours. External reviews typically take 45 days, or 72 hours for urgent cases. These are federal minimums — your plan may have faster timelines.

Atlas Rare drafts prior authorization appeal letters.

We pull your insurer's own coverage policy language, find the relevant PubMed citations for your condition, and generate a starting draft tailored to your specific denial. Your provider reviews it before submission. Currently in early access.

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