Approximately 25% of not-for-profits may lose their tax exempt status for failure to file a form – specifically the 990.
Before 2006, organizations with less than $25K in gross revenues were exempt from filing, but the law was changed to require those smaller organization to file an "electronic postcard" on new Form 990-N. It is a short process that entails typing in basic information about the organization (name, address, EIN) and stating that it has less than $25K of income for the year. Failure to enter that information online or file anything for three years now leads to revocation of exempt status.
Please click on the following link for further information: http://www.nytimes.com/2010/04/23/us/23exempt.html