HIV-1 seroconversion and subtype were evaluated, and factors associated with cohort retention were analyzed for subjects' baseline sociodemographic and behavioral characteristics in a 12-month follow-up study of injection drug users (IDUs). In November 2002, a community-based baseline survey was conducted to recruit 333 HIV-seronegative IDUs for a prospective cohort study in Xichang County of Sichuan Province, China. During the 12-month follow-up period, HIV incidence was 3.17 per 100 person-years (95% confidence interval [CI]: 0.98, 5.37), and all subtypes of 8 HIV-1 seroconversions were CRF_07BC. The retention rate at the 12-month follow-up visit was 70.3% (234 of 333 subjects). In a multiple logistic regression model, ethnicity (OR = 0.60, 95% CI: 0.34, 1.04) and appearing at the 6-month follow-up visit (OR = 9.03, 95% CI: 5.14, 15.89) were independently associated with retention. No drug-using or sexual behaviors were found to be associated with retention. This study confirmed one of drug-trafficking routes in mainland China, from Yunnan to Sichuan and then to Xinjiang. This study also suggested that HIV is spreading rapidly to more geographic areas along drug-trafficking routes in China, and a short-term follow-up rate may predict a long-term retention rate in this IDU cohort.