Young men who have sex with men (MSM) are at risk for HIV infection. We investigated inconsistent condom use among 827 sexually active young MSM (15-24 years), enrolled using venue-day-time sampling in Bangkok, Chiang Mai and Phuket, Thailand. Data was collected using palmtop computer-assisted self-interviewing. Of participants, 33.1% were regular MSM, 37.7% were male sex workers (MSWs) and 29.1% were transgenders (TGs). Of MSM, 46.7%, of MSWs, 34.9% and of TGs, 52.3% reported recent inconsistent condom use. In multivariate analysis, receptive anal intercourse (MSM, MSWs), receptive and insertive anal intercourse, living alone and a history of sexual coercion (MSWs), not carrying a condom when interviewed (MSM, TGs), lower education, worrying about HIV infection and a history of sexually transmitted infections (TGs) were significantly and independently associated with inconsistent condom use. Interventions for young MSM are needed and must consider the distinct risk factors of MSM, MSWs, and TGs.