The human immunodeficiency virus type 1 (HIV-1) epidemic in Taiwan is rapidly escalating because of an increasing number of injection drug users (IDUs). A molecular epidemiological study of HIV-1-infected IDUs in Taiwan was conducted from January 2004 to April 2005. Of the 131 HIV-1-positive specimens collected, all contained detectable sequences, including 105 from the C2-V3 region of env and 87 from the protease and reverse transcriptase genes of pol. Phylogenetic analysis of these sequences indicated that 128 individuals harbored CRF07_BC, which resembles the dominant strains circulating among IDUs in China. Twenty-three individuals had a history of travel to the southwest provinces of China and shared needles or apparatuses there. This suggests that CRF07_BC might have been transmitted from China into Taiwan, thereby causing an outbreak among IDUs in Taiwan. This is the first report in the English literature of the appearance of HIV-1 CRF07_BC in Taiwan. These provide information relevant to the development of antiviral therapy and vaccine in Taiwan and may assist public health workers in the prevention of HIV-1 spread.