The prevalence of urethral infection with Mycoplasma genitalium was determined by use of a DNA probe in 203 men attending a sexually transmitted disease clinic. M genitalium was detected in 3 (14%) of 21 with acute gonococcal urethritis; 3 (10%) of 30 with acute chlamydia-positive non-gonococcal urethritis (NGU); 4 (13%) of 31 with acute chlamydia-negative NGU; 10 (27%) of 37 with persistent or recurrent NGU; and 10 (12%) of 84 with no urethritis. The organism was more prevalent in homosexual (11 [30%] of 37) than in heterosexual men (19 [11%] of 166; p = 0.009). These data do not support an important aetiological role for M genitalium in acute urethritis, but suggest that it may account for some cases of NGU that become persistent or recurrent. The higher prevalence of urethral infection in homosexual men suggests that M genitalium may reside in the gastrointestinal tract.