BACKGROUND: Malaysia is experiencing severe problems with heroin dependence and HIV infection. This, study evaluated drug use and other HIV risk behaviors and their association with HIV and other infectious diseases in heroin-dependent subjects enrolled in a clinical trial of drug abuse treatment in Muar, Malaysia. METHODS: Baseline assessment of treatment-seeking subjects (n=177) included the Addiction Severity Index; AIDS Risk Inventory; serological tests for HIV, hepatitis B, and hepatitis C; and chest X-ray. RESULTS: All of the subjects were male; 67.8% were Malays, 28.8% Chinese, and 2.3%. Indian. Subjects had a mean (SD) age of 37.2 (9.1) years and 14.4 (8.5) years of using heroin; 76.3% reported lifetime injection drug use (IDU), and 41.5% reported current IDU; 30 of 156 (19.2%) tested HIV positive, 143 of 159 (89.9%) tested hepatitis C positive, and 25 of 159 (15.7%) had radiological evidence of pulmonary tuberbulosis. Malay subjects had a significantly higher prevalence of current IDU, needle sharing (p<0.01), and HIV infection (p<0.05) compared with Chinese subjects. Lifetime IDU, needle sharing, lack of consistent condom use, and Malay ethnicity were significantly associated with HIV infection. CONCLUSIONS: The high prevalence of HIV infection among heroin-dependent individuals, in Malaysia supports the important of interventions to reduce the major risk factors for HIV, including IDU, needle sharing, and unprotected sex.