List of non-profit religious organizations in the United States.

Thank you for your question.
 
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I went to a non profit directory site, choose religion as the focus
area and the United States as the country.  This yielded 1289 results.
The link is somewhat long, but is as follows:

http://www.idealist.org/en/ip/idealist/AdvancedSearch/Org/0:search?SID=e83797a426b830257f7e212bf6b68615&context-number=2&languageDesignation=en&assetType=Org&name=&keywords=&1.1.2=44&country=United+States&state=&city=&sortOrderings=name&1.16=Search

The IRS has the information you're looking for. It's called,
"Publication 78, Cumulative List of Organizations." The paper version
is available in most large public libraries, or through the Government
Printing Office. There is an online , searchable version available
here: http://apps.irs.gov/app/pub78
Or, you can download the whole thing from the IRS here:
http://www.irs.gov/pub/irs-utl/eopub78.zip