OBJECTIVE We used the hybrid capture assays to investigate the prevalence of human papillomavirus (HPV), Chlamydia trachomatis and Neisseria gonorrhoeae among commercial sex workers in Tokyo. METHODS Five hundred forty-six consecutive commercial sex workers (CSW) who visited an STD clinic for STD checkup in 1998 and 1999 were studied. A control group consisted of 233 consecutive women who visited a general gynecological clinic for annual checkup. A cervical sample was obtained for hybrid capture assays for HPV-A (low-oncogenic-risk types), HPV-B (intermediate- and high-oncogenic-risk types), C. trachomatis, and N. gonorrhoeae. Fisher's exact test was used for statistical analyses. RESULTS The positive rate for HPV-B among the CSW was 48.4%, significantly higher than the 6.0% among the control subjects. The positive rates for HPV-A, C. trachomatis, and N. gonorrhoeae were also significantly higher among the CSW than among the control subjects. Among the microorganisms tested, the positive rate for HPV-B was the highest in both the STD and control groups. CONCLUSIONS The high prevalence of HPV, C. trachomatis, and N. gonorrhoeae infection in CSW poses a risk of further transmission of STD to the general public, suggesting the need for further education and screening for CSW and the general public. We found high- and intermediate-oncogenic-type HPV to be the most prevalent infection among both CSW and control subjects. Screening for HPV may be necessary in STD and general clinics to predict the risk of cervical malignancy. Hybrid capture assays, which permit simultaneous detection of HPV and other STD with high sensitivity, may be a useful diagnostic method.