Background: Guidelines for testing men who have sex with men (MSM) were published in 2002. They did not recommend asymptomatic screening for urethral gonorrhoea or pharyngeal screening for chlamydia. To determine if these guidelines were appropriate, we audited gonorrhoea and chlamydia testing of MSM at our Centre. Methods: We carried out two audits at our Centre between August 2001 and July 2002. The first was an audit of testing MSM for gonorrhoea and/or chlamydia over 12 days. The second was an audit of all positive tests over this 12-month period for gonorrhoea or chlamydia among MSM. Results: During the 12 selected days 89 of 286 men tested (31%) were MSM. Among the MSM testing positive for gonorrhoea and/or chlamydia infection (15, 17%), symptomatic urethral infection was the most common (n = 8). No rectal and pharyngeal infections had site-specific symptoms. Based on the guidelines, 100 of the 334 tests ordered (30%) were not recommended according to the guidelines, and none of these 100 tests yielded a positive result. Over the 12-month audit period, 135 MSM were diagnosed with gonorrhoea and/or chlamydia. For gonorrhoea, site specific symptoms were present in 42 of 43 cases of urethral infection (98%), six of 23 cases of rectal infection (26%), and no cases of pharyngeal infection had symptoms. For chlamydia, site-specific symptoms were present in 29 of 48 cases of urethral infection (60%), six of 33 cases of rectal infection (18%), and in one of the two cases of pharyngeal chlamydia identified. A substantial proportion of cases occurred in clients with HIV infection (21, 16%). Conclusions: These findings strongly support screening among MSM and in particular not testing asymptomatic MSM for urethral gonorrhoea or any MSM for pharyngeal chlamydia.