CDC recommends screening of at-risk men who have sex with men (MSM) at least annually for urethral and rectal gonorrhea and chlamydia, and for pharyngeal gonorrhea. Although the standard method for diagnosis is culture, nucleic acid amplification (NAA) testing is generally more sensitive and favored by most experts. NAA tests have not been cleared by the Food and Drug Administration (FDA) for the diagnosis of extragenital chlamydia or gonorrhea and may not be marketed for that purpose. However, under U.S. law, laboratories may offer NAA testing for diagnosis of extragenital chlamydia or gonorrhea after internal validation of the method by a verification study. To determine sexually transmitted disease (STD) testing practices among community-based organizations serving MSM, CDC and the San Francisco Department of Public Health gathered data on rectal and pharyngeal gonorrhea and chlamydia testing at screening sites managed by six gay-focused community-based organizations in five U.S. cities during 2007. This report summarizes the results of the study, which found that three organizations collected samples for NAA testing and three for culture. In total, approximately 30,000 tests were performed; 5.4% of rectal gonorrhea, 8.9% of rectal chlamydia, 5.3% of pharyngeal gonorrhea, and 1.6% of pharyngeal chlamydia tests were positive. These results demonstrate that gay-focused community-based organizations can detect large numbers of gonorrhea and chlamydia cases and might reach MSM not being tested elsewhere. Public health officials could consider providing support to certain community-based organizations to facilitate testing and treatment of gonorrhea and chlamydia.