Form 990 and churches: who files and what still applies

Congress gives churches a set of special tax rules, and one of the best known is that churches don't file an annual information return. That is true, but only for organizations that are actually churches or that fit one of a few related categories. A church's affiliated school, hospital, camp or outreach ministry may have its own filing requirement, and the church itself still has tax obligations every year.

Who doesn't have to file a 990

The IRS excepts these religious organizations from filing Form 990, 990-EZ or 990-N (our guide to who must file lists the non-religious exceptions too):

• Churches, including synagogues, mosques, temples and other houses of worship, and interchurch organizations of local units of a church
• Conventions or associations of churches, such as denominational bodies
• Integrated auxiliaries of a church
• Church-affiliated organizations exclusively engaged in managing funds or maintaining retirement programs (but see the rules for supporting organizations)
• Schools below college level affiliated with a church or operated by a religious order
• Mission societies sponsored by or affiliated with churches, if more than half of their activities are conducted in, or directed at people in, foreign countries
• The exclusively religious activities of a religious order

The exception doesn't depend on size. A congregation with millions of dollars of receipts is not required to file, and neither is a house church with a few thousand.

What is an integrated auxiliary?

An integrated auxiliary is an organization related to a church that isn't a church itself. In general, it must be a 501(c)(3) public charity, be affiliated with a church or a convention or association of churches, and receive its financial support primarily from internal church sources rather than the public or government. Men's and women's organizations, seminaries, mission societies and youth groups that meet the first two requirements qualify whatever their sources of support.

An affiliated organization that sells services to the public and is funded mostly by fees or government grants usually is not an integrated auxiliary, and it may have its own filing requirement.

What a church still has to do

Form 990-T for unrelated business income

Being excused from the 990 doesn't excuse a church from Form 990-T. If a church has gross income of $1,000 or more in a year from a regularly carried on unrelated trade or business, it files a 990-T, due the 15th day of the 5th month after its year ends. Common examples are renting debt-financed property, selling advertising, and running a business open to the public that has no connection to the church's religious purpose. A church that is part of a larger body, such as a diocese, files its own 990-T if it has its own employer identification number (EIN).

A 501(c)(3) organization, including a church, must make its 990-T available for public inspection for three years.

Payroll and employment taxes

Churches generally must withhold, report and pay income tax and FICA (Social Security and Medicare) taxes for their employees, and file Form 941 (or Form 944 for some small employers) and Forms W-2. Churches are not liable for federal unemployment (FUTA) tax.

Ministers are treated differently. Wages paid to a duly ordained, commissioned or licensed minister for ministerial services are not subject to FICA withholding; the minister pays self-employment tax instead. A church isn't required to withhold income tax from a minister's pay, though the minister may ask for voluntary withholding. A church opposed to Social Security and Medicare taxes for religious reasons may elect out of employer FICA for non-minister employees by filing Form 8274, under strict timing rules. IRS Publication 517 covers clergy tax issues in detail.

Information returns for contractors

A church that pays an independent contractor, such as a musician, a contractor or a guest speaker who isn't an employee, files Form 1099-NEC when payments reach the reporting threshold. For payments made in 2026 and later, that threshold is $2,000; it was $600 for 2025 payments, and it may be adjusted for inflation starting in 2027. A minister who works as an independent contractor rather than an employee is reported on a 1099 too.

State and local rules

States set their own rules. Many exempt churches and religious organizations from charitable solicitation registration, but property tax exemptions, sales tax exemptions and annual reports to the secretary of state each have their own requirements. A church incorporated as a nonprofit corporation often still files the state's corporate annual report. Our state charity filings guide explains how state reporting generally works.

Church-related organizations that do file

Many organizations with a religious mission are not churches in the tax sense. They generally file a return in the 990 series like any other exempt organization, choosing among the 990-N, 990-EZ and Form 990 by size:

• Religious organizations that aren't churches, including many parachurch ministries: broadcast ministries, campus ministries, relief and development agencies, publishers and camps
• Church-affiliated colleges and universities, because the school exception covers only schools below college level
• Church-affiliated hospitals and health systems, which are not on the exception list (hospitals that file Form 990 also complete Schedule H)
• Social service agencies, such as a denominational family services organization funded by government contracts, unless they truly qualify as integrated auxiliaries
• Supporting organizations, which have their own filing rules

If you are not sure whether your ministry is a church, an integrated auxiliary or a separate religious organization, it is worth settling the question. A religious organization that should have been filing faces the same automatic revocation after three missed years as any other nonprofit. If returns were missed, catching up before the third year is far easier than reinstatement.

Filing voluntarily

Some churches choose to file a Form 990 for transparency, to satisfy a grantmaker or lender, or because a denomination encourages it. That is allowed, but the IRS instructions are clear: an organization that isn't required to file but chooses to do so must file a complete return, with all the information and schedules required. A voluntary return is also open to public inspection like any other.

Similarly, churches don't have to apply for recognition of exemption, but many do so voluntarily on Form 1023 for the assurance a determination letter gives donors. A church that applies pays the user fee like any other applicant.

990IRS.com is a private company, not the IRS. This page is general information, not legal or tax advice for your organization. Example organizations and figures are hypothetical.