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The Centers for Disease Control and Prevention recommends that men who have sex with men (MSM) be screened annually for gonorrhea (GC) infection at the urethral, pharyngeal, or rectal site based on recent sexual exposure. This evaluation estimated the proportion of GC infections in MSM that would be missed if only urethral or urine specimens were tested.Culture of specimens from all sites and urethral (or urine) nucleic acid amplification test (NAAT) results for gonorrhea were reviewed for all identified MSM attending the San Diego County STD Clinic during 1997–2003.During the 7-year period, 7333 MSM were tested for GC and 1157 (15.8%) had a positive test result at ≥1 sites. Overall, 10.8% of urethral, 9.8% of rectal, and 4.0% of pharyngeal tests were positive. Among 5812 patients who had a urethral and a rectal or pharyngeal specimen tested, 970 were positive and among those, 369 (38%) had a negative test result in their urethral or urine specimen. Among 163 patients who had only a rectal and/or pharyngeal specimen tested for GC, 16 (9.8%) were positive. If the clinic had tested only urethral or urine specimens, 33% of total gonorrhea cases among MSM [385 (369 + 16) of 1157] would have been missed.GC screening strategies for MSM should include testing of rectal and pharyngeal specimens based on exposure. Given the decline of culture availability, efforts are needed to encourage laboratories to validate NAATs for rectal/pharyngeal specimens, which will likely increase exposure-based screening of MSM.