In this study 1155 injection drug users receiving targeted intervention in five cities of Punjab were surveyed; three cities (Amritsar, Taran-Taran, Batala) were in districts sharing international border with Pakistan and the rest two were Jalandhar and Ludhiana. Information on socio-demography, substance use and sexual practices were collected; blood samples were tested for biologic markers. HIV and HCV antibody (HCVAb) prevalence in injection drug users were 29 and 49%, respectively. Of the HCVAb seroreactive injection drug users, 33% had HIV as well. HIV prevalence in young injection drug users (≤19 years), estimated as surrogate for HIV incidence, was high at 12% and HCVAb in this subgroup was 27%. Herpes simplex virus 2 antibody (IgG) was detected in 10% injection drug users; 2% had syphilis. Alcohol use prevalence was high and frequency of use concerning. In multivariate analyses, ‘city of residence closer to international border’ and ‘>1 year duration of injecting drug’ were associated with HIV and HCVAb. Furthermore, ‘irregular supply of syringes and needles’ was associated with HCVAb seroreactive status of injection drug users (adjusted odds ratio 1.7; 95% CI 1.3–2.3; P < 0.001), and ‘any genital disease symptom within the last year’ (adjusted odds ratio 2; 95% CI 1.4–2.9; P < 0.001) was associated with HIV infection. Alcohol and sexual risk reduction; strengthening of needle–syringe exchange; reducing injecting duration and clinical management of HIV, HCV and HIV/HCV co-infection appear as four core program needs.