There is a difference between registration and filing. Tax-exempt organizations with more than $5,000 in annual gross receipts must register with IRS, but they don't have to file the annual information report until they reach annual gross receipts of $25,000. Religious congregations have automatic Section 501(c)(3) status and are not required to register or file. Foundations of any size must register and file.
Nonprofit organizations with over $25,000 in annual gross receipts are required to file Form 990 with the IRS. Organizations that have gross receipts between $25,000 and $100,000 and less than $250,000 in total assets at the end of the year can opt to file a shorter form called Form 990-EZ. Private foundations of any size file Form 990-PF. Since some funders require Form 990, some smaller nonprofit organizations do file Form 990 even though they are not required to do so by the IRS.
On Form 990, "gross receipts" include all revenue received by the organization. It is defined as the total of "Rental Expenses" (line 6b) + "Cost or other basis and sales expenses" (line 8b)+ "Direct special event expenses other than fundraising expenses" (line 9b) + "Cost of goods sold" (line 10b) + "Total Revenue" (line12).
New Filing Thresholds
In 2008, new filing thresholds took effect. These thresholds change for the next three years. For details, see the IRS website at: http://www.irs.gov/charities/article/0,,id=184445,00.html.