Transgender people are at high risk of sexually transmitted viruses such as hepatitis B virus (HBV) and human immunodeficiency virus (HIV). Moreover, Indonesia has a moderate to high rate of HBV infection and a rapid epidemic growth of HIV. Because hepatitis C virus (HCV) can co-occur with HBV and HIV, it was also evaluated in this study. Ten of 107 individuals (9.3%) were Hepatitis B surface antigen (HBsAg) positive and/or HBV DNA positive, whereas nineteen of 101 individuals (18.8%) with negative HBsAg were Hepatitis B core antibody (anti-HBc)-positive. Seven of 107 individuals (6.5%) were anti-HCV positive, and sixteen of 100 tested samples (16%) were HIV positive. Genotype and subtype analyses of all ten HBV DNA (six HBsAg positive and four anti-HBc positive) strains showed that three were HBV genotype/HBsAg subtype C/adrq+, one was C/adw2, and five were B/adw2. The HCV subtype distribution showed that 33.3% were HCV-1b, and 66.7% were HCV-3k (n=6). These distributions differed from those found in the general population of Surabaya, Indonesia. The HIV subtype analysis showed that, interestingly, a high prevalence of HIV, with possible recombinants of CRF01_AE and subtype B, were found.