Many male transvestites (waria) in Jakarta, Indonesia engage in unprotected receptive anal and oral intercourse with homosexual and bisexual men for pay. Although this behaviour clearly puts them at risk of sexually transmitted diseases (STDs), including HIV infection, little is known about the prevalence of STD among them. To learn the STD prevalence and its risk factors, we conducted an STD prevalence survey among waria in North Jakarta, Indonesia. From August to December 1999 we offered screening for rectal and pharyngeal infections with Neisseria gonorrhoeae (Ng), Chlamydia trachomatis (Ct) by DNA probe (GenProbe PACE 2) and for Treponema pallidum (Tp) by non-treponemal and treponemal serological tests. Of 296 participants (median age 28 years), 93% reported having been paid for sex. A total of 96% reported having had oral sex (median five times/week) and/or anal sex (median three times/week) in the last week. Ng was found in the rectum of 12.8% and the pharynx of 4.2%; Ct was found in 3.8% and 2.4%, respectively. A total of 43.6% had reactive non-treponemal and treponemal tests. Of the 129 with positive treponemal tests, 42.6% had non-treponemal test titres greater than 1:8. In the logistic regression model, waria who were younger (≤25 years old) had a significantly 3.5 times risk of Ng and/or Ct infections than older waria (>25 years old). Because only 12% of waria stated that they consistently used condoms during any sex act, it is important to warn them that STD/HIV transmission can occur with either anal or oral sex and that the risk of either anal or oral transmission can be reduced by condom use. In addition, high rates of asymptomatic syphilis and rectal gonorrhoea warrant a periodic screening and treatment for these infections in this population. Because waria have the highest rates of HIV and their clients consist of homosexual and bisexual men, successful prevention efforts in waria could help curb the spread of the epidemic.