Behavioral surveillance was undertaken among 1,150 male-to-female transgenders (waria) in Java, Indonesia, 2007; samples were collected for HIV and STI testing (n = 748). Almost all waria had ever sold sex (median duration 10 years). Prevalence of HIV was 24.4%, syphilis 26.8% and rectal gonorrhea and/or chlamydia 47.0%. Syphilis and rectal STIs were associated with HIV infection. Consistent condom use during receptive anal sex with clients was reported by 35.9% waria and was higher among those who visited an STI clinic and who knew their HIV status. Efforts should continue to strengthen behavior change and STI care in future HIV prevention programs.