There is little research on injecting drug use in Nigeria. We investigated the prevalence of HIV, hepatitis B and C, and sexually transmitted infections (STIs) among male injection drug users (IDUs) in Lagos. Male IDUs (N 328) were recruited through respondent-driven sampling. Participants completed an interview about their sexual and injecting risk behaviours and were tested for hepatitis B surface antigen (HBV), hepatitis C antibody (HCV), HIV and syphilis, as well as genital chlamydia and gonorrhoea infections. Three-quarters of IDUs (74%) reported injecting drugs in the past one month although most did not share needles (92%) and the majority obtained sterile needles from pharmacists (87%). Estimated HBV, HCV, HIV, syphilis, gonorrhoea and chlamydia prevalences were 7.8%, 7.7%, 0.9%, 1.9%, 0.0%, and 3.7%, respectively. The burden of HIV is presently low among IDUs in Lagos. Changes in accessibility to sterile needles at pharmacists would likely have a deleterious effect on IDUs’ health. HBV vaccination and HCV prevention programmes for IDUs are urgently needed.