The aim of this study was to estimate the detection rates of Mycoplasma and Ureaplasma, which are presumptive causes of sexually transmitted diseases (STDs), in young men in Sapporo, Japan. In addition, we examined the associations among Chlamydia trachomatis, Mycoplasma, and Ureaplasma. A survey of 100 asymptomatic healthy male volunteers was carried out. C. trachomatis, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum in first-voided urine specimens were detected by polymerase chain reaction assay. Detection rates were 1% for M. genitalium, 4% for M. hominis, 12% for U. urealyticum, and 23% for U. parvum. C. trachomatis was detected in 6% of samples. No M. hominis, U. urealyticum, or U. parvum was detected simultaneously in any sample positive for C. trachomatis. The detection rate of urinary M. genitalium was extremely low, which is similar to previous reports from Japan. The detection rates of urethral U. urealyticum and U. parvum were significantly related to sexual activity. We need to determine whether these pathogens have a role in the sexual transmission of disease or just in colonization.