OBJECTIVE: An explosive outbreak of HIV-1 circulating recombinant form (CRF) 07_BC among injection drug users (IDUs) in Taiwan was first reported in 2004 and reach the peak in 2005. The objectives of this study were to investigate the molecular epidemiology of different HIV-1 subtypes and their associated risk factors among Taiwanese IDUs in 2004 and 2005. METHODS: Questionnaires and blood specimens were collected from inmates from 4 detention centers and 2 prisons. HIV-1 subtypes were determined using nested polymerase chain reactions with multiplex primers and phylogenetic analyses. A case-control study was conducted to elucidate risk factors associated with CRF07_BC infection. RESULTS: A total of 93.8%, 4%, and 2.2% of 451 inmates with IDU history were infected with CRF07_BC, subtype B, and CRF01_AE, respectively. Besides CRF07_BC, a new outbreak of CRF01_AE infection was identified among IDUs from central region. Multivariate analysis showed that sharing dissolved heroine solution [odds ratio (OR) = 17.2], sharing syringes (OR = 34), number of persons sharing syringes (2 vs. 1, OR = 3.1), and lower educational level (OR = 2.3) were risk factors associated with CRF07_BC infection. CONCLUSIONS: Sharing dissolved heroine solution is a neglected risk factor associated with HIV-1 infection and it should be emphasized in the AIDS education and harm reduction programs immediately.