Generally, tax-exempt organizations must file an annual information return Form 990 “Return of Organization Exempt from Income Tax,” whose annual receipts are "normally" more than $25,000 a year. It is an information return and not an income tax return since the organizations that file it do not pay income taxes (except, as explained below, in certain cases an organization may have to pay an “unrelated business income tax”).. Tax-exempt organizations that have annual gross receipts not normally in excess of $25,000 are not required to file the annual information return. In addition, churches and certain religious organizations, certain state and local instrumentalities, and other organizations are exempted from the annual return filing requirement.

Form_990-EZ, Short Form Return of Organization Exempt From Income Tax. The Form 990-EZ is designed for use by small tax-exempt organizations and nonexempt charitable trusts. An organization may file Form 990-EZ, instead of Form 990, only if (1) its gross receipts during the year were less than $100,000, and (2) its total assets (line 25, Column (B) of Form 990-EZ) at the end of the year were less than $250,000.

Form 990, Form 990-EZ, or Form 990-PF must be filed by the 15th day of the 5th month after the end of your organization's accounting period. The instructions for these forms indicate the Service Center to which they must be sent.

A tax-exempt organization that fails to file a required return is subject to a penalty of $20 a day for each day the failure continues. The same penalty will apply if the organization fails to give correct and complete information or required information on its return. The maximum penalty for any one return is the lesser of $10,000 or 5 percent of the organization's gross receipts for the year. If the organization has gross receipts in excess of $1,000,000, the penalties are increased to $100 per day with a maximum penalty of $50,000.

Even though an organization is recognized as tax exempt, it still may be liable for tax on its unrelated business income. An exempt organization that has $1,000 or more gross income from an unrelated business must file Form_990-T, Exempt Organization Business Income Tax Return. The obligation to file Form 990-T is in addition to the obligation to file the annual information return. Tax-exempt organizations must make quarterly payments of estimated tax on unrelated business income. An organization must make estimated tax payments if it expects its tax for the year to be $500 or more. The Form 990-T of a tax-exempt organization must be filed by the 15th day of the 5th month after the tax year ends. An employees' trust must file Form 990-T by the 15th day of the 4th month after its tax year ends. A tax-exempt organization's Form 990-T is not available for public inspection. For additional information, download Publication 598, Tax on Unrelated Business Income of Exempt Organizations.
Every employer, including a tax-exempt organization, who pays wages to employees is responsible for withholding, depositing, paying, and reporting federal income tax, social security taxes (FICA), and federal unemployment tax (FUTA) for such wage payments, unless that employer is specifically excepted by statute from such requirements or if the taxes are clearly inapplicable.