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To investigate the incidence rates of HIV, hepatitis C virus (HCV), and hepatitis B virus (HBV) among injection drug users (IDU) in a drug trafficking city in southwest China.A prospective cohort study.A cohort of 333 HIV-seronegative IDU was followed for 36 months from November 2002 and evaluated every 6 months for seroconversions to HIV and HCV antibodies as well as hepatitis B surface antigen. Questionnaire interviews were conducted to collect information about risk behaviors.Some 68.8% of subjects completed the last follow-up survey. A total of 14 HIV, 47 HCV and 51 HBV seroconversions were observed over the 36-month follow-up period, yielding average incidence rates of 2.3 per 100 person-years for HIV, 33.3 for HCV and 11.3 for HBV. Multivariate Poisson regression analyses showed that factors independently associated with HIV seroconversion were minority ethnicity and greater frequent sharing of needles or syringes in the past 3 months one or more times per week. Predictors of HCV seroconversion included being female, greater frequent drug use in the past 3 months seven or more times per week, and frequent sharing of needles or syringes in the past 3 months one or more times per week.Blood-borne infections continue to spread, but at lower rates with time among IDU in a southwestern Chinese city where intervention programmes have existed for a few years. Rigorous implementation of harm reduction programmes may have reduced seroconversion to blood-borne infections among targeted high-risk populations.