The aim of this study was to estimate the incidence rates of asymptomatic sexually transmitted infections (STI) in young men in Sapporo, Japan. A survey of 204 healthy male volunteers was conducted. First-voided urine specimens were used for detection of Chlamydia trachomatis and Neisseria gonorrhoeae with polymerase chain reaction assay, and cotton swab wiping of the external genitalia was used for detection of human papillomavirus (HPV) with the Hybrid Capture method. The incidence rates were 3.4% for C. trachomatis and 5.9% for HPV. No N. gonorrhoeae was detected. In sexually active men who had regular sexual intercourse, the detection rate of C. trachomatis was 4.7% and that of HPV was 8.0%. Our study showed that the incidence rates of asymptomatic STIs were not negligible, and that we should provide screening programs for young men with a high risk for such unrecognized infections and study their natural histories.