If your church runs a nonprofit agency, you may want to check this state-by-state list of 275,000 organizations whose tax-exempt status was recently automatically revoked by the IRS. Most organizations on the list no longer exist but some still do.
One organization on the list that still exists is a community development agency run by St. James Chapel Church of God in Christ, according to a newspaper in Reading, PA.
A law in 2006 requires most tax-exempt organizations (excluding churches) bringing in $25,000 or less to start filing yearly IRS returns, specifically form 990-N. Before 2006, they were not required to file. Those that do not file for three consecutive years will find their tax-exempt status automatically revoked by the IRS.
If an organization run by, or affiliated with, your church is on the list of organizations that lost tax-exempt status, an application can be filled out to reinstate it.