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Asymptomatic Chlamydia trachomatis (CT) infection and other sexually transmitted infections in men potentially contribute significantly in sustaining the spread of the infection. To describe the distribution and related sexual behaviors, we conducted a cross-sectional study among young Thai men using a (1:30) systematic sampling of all newly inducted military conscripts in Thailand.In November 2008 and May 2009, participants’ urine and serum samples were tested for CT and Neisseria gonorrhoeae, using a multiplex polymerase chain reaction technique, and serologic testing for Treponema pallidum and HIV-1 was done. Information on demographic data and risk behaviors was obtained by a self-administered questionnaire.The overall prevalence rates of CT, N. gonorrhoeae, HIV-1, and syphilis infection were 7.9%, 0.9%, 0.5%, 0.05%, respectively. The risk factors for CT infection were living in the upper north region (adjusted rate ratios [95% confidence interval], 2.13 [1.39–3.26]), having had 4 or more sexual partners (2.14 [1.48–3.09]), graduation from a vocational school (1.66 [1.14–2.41]), inconsistent condom use (1.48 [1.05–2.08]), unemployment (1.82 [1.06–3.12]), and age 21 years or younger (1.63 [1.01–2.63]).The prevalence of CT infection among young male military conscripts was high, especially among men from upper northern Thailand. Multiple sexual partners, graduation from a vocational school, inconsistent condom use, unemployment before the military induction, and younger age were independently associated with the CT infection among young Thai men. These data will be useful to develop more effective public health interventions to prevent, detect, and treat sexually transmitted infections among young men in Thailand.