This study aimed to measure risk behaviours and seroprevalence of HIV and hepatitis C virus in IDUs in Manipur, North-East India, and evaluate the impact of the recently established Syringe and Needle Exchange Program (SNEP). Sampling strategy was based on social networks. Peer interviewers administered the study questionnaire and collected blood for anti-HCV and anti-HIV testing. One hundred and ninety-one IDUs (85% male) took part. Average age at first injection was 19 years and average length of time injecting was 3.7 years. The main drug currently injected was heroin (66%). Most (93%) reported having shared injecting equipment and only 42% had used the SNEP. Three-quarters (74.7%) were infected with HIV and almost all (98%) with HCV. Age (p < 0.001) and length of time injecting (p < 0.001) were significantly associated with being HIV-positive. Over two-thirds were sexually active, but only 3% consistently used condoms. Almost three-quarters of IDUs in this study were infected with HIV, most within the first two years of injecting, indicating infection continues to spread at very high rates. Unsafe sexual practices place partners of infected IDUs at risk of infection. The SNEP must increase its coverage to young and new IDUs before they are exposed to blood-borne viruses.