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Nonprofit annual filing: which Form 990, when it’s due, and how an organization loses its exemption

Most tax-exempt organizations owe the IRS something every year, even when they owe no tax. The form depends on size, the deadline is the same for nearly everyone, and three missed years in a row cost an organization its exemption automatically — with no appeal.

Last reviewed September 2026 · General information, not advice for your situation

In short

  • Every organization exempt under section 501(a) must file an annual return unless an exception applies — churches and their integrated auxiliaries are the best-known one (IRC §6033(a)(1), (a)(3)(A)).
  • Which form generally depends on size: Form 990-N if gross receipts are normally $50,000 or less; Form 990-EZ (or, by choice, Form 990) if gross receipts are under $200,000 and total assets under $500,000; otherwise Form 990. Private foundations file Form 990-PF regardless (IRS).
  • The return is due by the 15th day of the 5th month after the year ends — May 15 for a calendar year — and Form 8868 gives an automatic 6-month extension for Forms 990, 990-EZ and 990-PF, but not for the 990-N (IRS).
  • A late or incomplete Form 990 or 990-EZ costs $25 a day, up to the lesser of $13,000 or 5% of gross receipts, for returns required to be filed in 2026 — $130 a day, up to $65,000, if gross receipts exceed $1,309,500 (Rev. Proc. 2024-40 §2.54).
  • Fail to file for three consecutive years and exemption is revoked automatically, from the due date of the third return (IRC §6033(j)(1)(B)). Getting it back takes a new application (IRC §6033(j)(2)).

Who has to file

The starting point is broad: every organization exempt from tax under section 501(a) must file an annual return (IRC §6033(a)(1)). That includes an organization that hasn’t yet applied for recognition of exemption, if it meets the filing thresholds (Instructions for Form 990 (2025), Section A). Owing no tax doesn’t remove the filing requirement.

The main exceptions:

  • Churches and religious activities. Churches, their integrated auxiliaries, conventions or associations of churches, and the exclusively religious activities of a religious order are excepted by the statute itself (IRC §6033(a)(3)(A)). The regulations add others, such as certain church-affiliated mission societies and schools below college level (Treas. Reg. §1.6033-2(g)(1)).
  • Certain government-related organizations. A state institution whose income is excluded under section 115, a governmental unit or affiliate of a governmental unit described in Rev. Proc. 95-48, and a section 501(c)(1) organization don’t file Form 990 or 990-EZ (Instructions for Form 990 (2025), Section B).
  • Small organizations don’t file Form 990 or 990-EZ, but most must still submit the Form 990-N e-Postcard instead (below) (Instructions for Form 990 (2025), Section B).

The exceptions have conditions and cross-exceptions. For example, a section 509(a)(3) supporting organization must file Form 990 or 990-EZ even if its gross receipts are normally $50,000 or less, and even if it is a governmental affiliate, unless it qualifies for another listed exception (Instructions for Form 990 (2025), Section A). Whether an exception applies depends on the organization’s facts.

Which form: 990-N, 990-EZ, 990 or 990-PF

Which form an organization files generally depends on its financial activity (IRS):

OrganizationForm
Gross receipts normally $50,000 or lessForm 990-N (e-Postcard) — or, by choice, a full Form 990-EZ or 990
Gross receipts under $200,000 and total assets under $500,000Form 990-EZ, or by choice Form 990
Gross receipts of $200,000 or more, or total assets of $500,000 or moreForm 990
Private foundation, whatever its sizeForm 990-PF

Thresholds as stated by the IRS and in the 2025 Form 990 instructions.

“Gross receipts” means the total received from all sources during the year, without subtracting any costs or expenses (Instructions for Form 990 (2025), Section A) — so an organization with modest net income can still be over a threshold. For Form 990-EZ, the test is gross receipts for the year and total assets at the end of the year (Instructions for Form 990 (2025), Section A).

What “normally” means for the 990-N. Gross receipts are normally $50,000 or less if the organization is up to a year old and received, or donors pledged, $75,000 or less in its first tax year; is between 1 and 3 years old and averaged $60,000 or less in each of its first 2 tax years; or is at least 3 years old and averaged $50,000 or less over the immediately preceding 3 tax years, including the current one (Instructions for Form 990 (2025), Appendix B).

Some organizations can’t use the shorter forms whatever their size. Sponsoring organizations of donor advised funds must file Form 990, not Form 990-EZ, and so must a controlling organization under section 512(b)(13) that transferred funds with a controlled entity during the year (Instructions for Form 990 (2025), Section A). An organization eligible for a shorter form that chooses to file Form 990 must file a complete return (Instructions for Form 990 (2025), Section A).

The e-Postcard asks for basic information only — EIN, tax year, legal name and address, other names used, a principal officer, website, confirmation that gross receipts are $50,000 or less, and whether the organization has terminated — and is submitted electronically only; there is no paper form (IRS). The duty to submit it comes from the statute (IRC §6033(i)).

When it’s due, and the extension

The annual return is due on or before the 15th day of the fifth month after the close of the year (Treas. Reg. §1.6033-2(e)). For a calendar-year organization that is May 15 of the following year; a due date falling on a Saturday, Sunday or legal holiday moves to the next business day (Instructions for Form 990 (2025), Section E). An organization that liquidates, dissolves or terminates files by the 15th day of the 5th month after that event (Instructions for Form 990 (2025), Section E).

Extension. Filing Form 8868 by the due date gives an automatic six-month extension of time to file Form 990, 990-EZ or 990-PF (Treas. Reg. §1.6081-9(a), (b); IRS). The Form 990-N due date can’t be extended (IRS), and the e-Postcard can’t be filed until the tax year has ended (IRS).

Electronic filing is required. The statute says any organization required to file a return under section 6033 must file it electronically (IRC §6033(n)), and the instructions confirm that 2025 Forms 990 and 990-EZ must be e-filed (Instructions for Form 990 (2025), Section E; Instructions for Form 990-EZ (2025), Section D). An organization required to e-file that sends paper is treated as not having filed, even though a paper return was submitted (Instructions for Form 990 (2025), Section H).

Catching up on old years works differently: e-filing is available only for the current tax year and the 2 prior tax periods, and a return outside that window is filed on paper (Instructions for Form 990 (2025), Section E).

Penalties for late or incomplete returns

The penalty applies both to a return not filed on time (counting any extension) and to a return that leaves out required information or shows incorrect information (IRC §6652(c)(1)(A)). It runs for each day the failure continues. The dollar amounts in the statute are adjusted for inflation by the year the return is required to be filed (IRC §6652(c)(7)):

Return required to be filed inDaily penaltyMaximum per return
2026 — most organizations$25Lesser of $13,000 or 5% of gross receipts for the year
2026 — gross receipts over $1,309,500$130$65,000
2027 — most organizations$25Lesser of $13,000 or 5% of gross receipts for the year
2027 — gross receipts over $1,339,500$130$66,500

2026 figures: Rev. Proc. 2024-40 §2.54. 2027 figures: Rev. Proc. 2025-32 §4.53.

Sources for the table: Rev. Proc. 2024-40 §2.54 (2026) and Rev. Proc. 2025-32 §4.53 (2027). For example, a calendar-year 2025 return, due May 15, 2026, falls in the 2026 row.

“Incomplete” counts. The IRS can charge the penalty for a return that skips a required line or a required part of a schedule, or that contains incorrect information — its example is reporting contributions net of related fundraising expenses (Instructions for Form 990 (2025), Section H). Using a paid preparer doesn’t relieve the organization of responsibility for a complete and accurate return (Instructions for Form 990 (2025), Section H).

Individuals can be penalized too. If the IRS makes a written demand for the return or missing information and the deadline it sets passes, the person failing to comply — an officer, director, trustee, employee or other individual under a duty to file (IRC §6652(c)(6)(C)) — owes $10 a day (IRC §6652(c)(1)(B)), capped at $6,500 on all persons for any one return for returns required to be filed in 2026 and 2027 (Rev. Proc. 2024-40 §2.54; Rev. Proc. 2025-32 §4.53).

Reasonable cause. No penalty applies if the failure is shown to be due to reasonable cause (IRC §6652(c)(5)). A late return should include an explanation of the reasons (Instructions for Form 990 (2025), Section E). Whether a reason is enough depends on the facts.

The 990-N has no late penalty — but missing it still counts toward automatic revocation (IRS).

Three missed years: automatic revocation

An organization that fails to file its required annual return or notice — Form 990, 990-EZ, 990-PF or the 990-N — for 3 consecutive years loses its exemption automatically, on and after the due date of the third return (IRC §6033(j)(1)(B)). The IRS describes the effective date as the original filing due date of the third annual return or notice (IRS). After 2 missed years, the statute requires the IRS to notify the organization that its exemption will be revoked if it also misses the next return or notice (IRC §6033(j)(1)(A)).

There’s no appeal: the IRS says the law prohibits it from undoing a proper automatic revocation (IRS).

What revocation means (IRS):

  • The organization is no longer exempt from federal income tax, and may have to file an income tax return (Form 1120 or Form 1041) and pay tax.
  • It can no longer receive tax-deductible contributions, and is removed from the IRS’s cumulative list of tax-exempt organizations (Publication 78). Donors can deduct contributions made before the organization appears on the Automatic Revocation List.
  • Its name goes on the public Automatic Revocation List, which the IRS publishes and updates monthly; the statute requires the IRS to maintain that list (IRC §6033(j)(1)(B)).
  • State and local laws may also affect an organization that loses its exemption.

Getting exemption back: reinstatement

A revoked organization must apply for reinstatement, even if it was never required to apply for exemption in the first place (IRC §6033(j)(2)). If it shows reasonable cause, the IRS may, at its discretion, reinstate it retroactive to the revocation date (IRC §6033(j)(3)). Rev. Proc. 2014-11 sets out four routes. For the three retroactive routes, the 15-month line is measured from the later of the date of the revocation letter or the date the IRS posted the organization’s name on the Revocation List (Rev. Proc. 2014-11 §§4.01, 5.01, 6.01); the fourth route has no time limit:

  1. Streamlined retroactive reinstatement. For an organization that was eligible to file Form 990-EZ or 990-N for each of the three missed years and has never been automatically revoked before. It applies within 15 months, with the user fee, and is treated as having reasonable cause if approved (Rev. Proc. 2014-11 §4.01–.02).
  2. Retroactive reinstatement within 15 months. For everyone else applying within 15 months. The application must include a reasonable cause statement for at least one of the three years, and the organization must file paper annual returns for the three years and any later unfiled years (Rev. Proc. 2014-11 §5.01, §8.01).
  3. Retroactive reinstatement after 15 months. The same requirements, except reasonable cause must be shown for all three years (Rev. Proc. 2014-11 §6.01, §8.02).
  4. Reinstatement from the post-mark date. An application with the user fee, but exemption runs only from the date the application is post-marked — not back to the revocation date (Rev. Proc. 2014-11 §7.01).

Under the three retroactive routes, the IRS won’t impose the §6652(c) late-filing penalty for the three years that caused the revocation, if the organization meets that route’s conditions, including filing the required paper returns (Rev. Proc. 2014-11 §§4.03, 5.02, 6.02).

Reasonable cause here means the organization exercised ordinary business care and prudence in trying to meet its filing requirement; the statement must describe the facts that led to the failure, how it was discovered, and the steps taken to prevent it happening again, and the IRS weighs all the facts and circumstances (Rev. Proc. 2014-11 §8.03–.04).

Whether an organization qualifies for a retroactive route, and whether its reasons amount to reasonable cause, turns on its own facts. The gap between the revocation date and the reinstatement date can matter for donors and for any tax owed in the meantime. A reinstated organization can be revoked again if it misses three more consecutive years, and can’t use the streamlined route a second time (IRS).

Public inspection, and what stays private

A 501(c) organization’s annual return is a public document. It must make its return available for inspection at its principal office and give a copy to anyone who asks in person or in writing, charging no more than reasonable copying and mailing costs (IRC §6104(d)(1)). The duty covers each return for 3 years from its due date, including extensions (IRC §6104(d)(2)). Copies needn’t be provided on request if the return is “widely available” online, but the return must still be available for inspection (Instructions for Form 990 (2025), Section J).

Donor names. An organization that isn’t a private foundation or a political organization doesn’t have to disclose the names or addresses of its contributors (IRC §6104(d)(3)(A)). The rest of Schedule B — amounts, descriptions of noncash gifts and other information — must be made available unless it clearly identifies the contributor (Instructions for Form 990 (2025), Appendix D).

For boards: Form 990 asks whether a complete copy of the final return was given to every voting board member before it was filed (Instructions for Form 990 (2025), Part VI, line 11a). The answer is public along with everything else.

Common questions

Does a small nonprofit with no income have to file anything?

Usually yes. An organization whose gross receipts are normally $50,000 or less generally must submit the Form 990-N e-Postcard if it doesn’t file Form 990 or 990-EZ (Instructions for Form 990 (2025), Appendix B). Churches and certain other organizations are excepted (IRC §6033(a)(3)(A)).

When is Form 990 due?

By the 15th day of the 5th month after the organization’s year ends — May 15 for a calendar year. Form 8868 gives an automatic 6-month extension for Forms 990, 990-EZ and 990-PF; the 990-N can’t be extended (IRS).

What is the penalty for filing Form 990 late?

For returns required to be filed in 2026, $25 a day, up to the lesser of $13,000 or 5% of gross receipts; for organizations with gross receipts over $1,309,500, $130 a day up to $65,000 (Rev. Proc. 2024-40 §2.54). The same penalty can apply to an incomplete return, and it doesn’t apply if the failure was due to reasonable cause (IRC §6652(c)). There is no late penalty for the 990-N (IRS).

Our exemption was automatically revoked. Can we appeal?

No — the IRS says the law prohibits it from undoing a proper automatic revocation and provides no appeal process; the organization must apply for reinstatement (IRS). Retroactive reinstatement is available in some cases, generally depending on timing and reasonable cause (Rev. Proc. 2014-11).

Are donations still deductible after revocation?

A revoked organization isn’t eligible to receive tax-deductible contributions, but donors can deduct contributions made before its name appears on the Automatic Revocation List (IRS).

Sources

This guide is general information about how the rules work, last reviewed September 2026. It is not tax, legal or financial advice for your circumstances, and reading it doesn't create a client relationship. Tax rules, figures and thresholds change, and how they apply depends on your facts — talk to a tax professional before acting on anything here.

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