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Male commercial sex workers are one of the high risk community for blood borne viruses. However, there no data concerning the molecular status of Human Immunodeficiency Virus (HIV), Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) circulated among male commercial sex workers with injecting drug habits. Blood samples obtained from injecting drug male commercial sex workers in Surakarta were examined for HIV antibodies, HBsAg and HCV antibodies, respectively, by immunological assays. Blood samples were also subjected for viral nucleic acid extraction and molecular detection of HIV, HBV and HCV by nested (RT) PCRs. The PCR products were purified from agarose gels, and the nucleotide sequences were retrieved and molecular analyzed. HIV, HBV and HCV were detected in 29.4% (10/34), 17.6% (6/34) and 52.9% (18/34), respectively. HIV CRF01_AE and B were found to be circulating in the community. HBV genotype B3 was predominated, followed by C1. HCV genotype 1a was predominated, followed by 1c, 3a, 1b and 4a. HIV, HBV and HCV were found circulating in the male commercial sex workers with injecting drug habits in Surakarta, Indonesia.