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In the UK, needle and syringe programmes (NSP) are delivered via community pharmacies or substance misuse services (SMSNSP). Understanding the profile of drug injectors primarily using different sources of injecting equipment can help service design.Blood spot samples and behavioural data were collected from drug injectors and tested for antibodies to hepatitis C and hepatitis B. Data were analysed in relation to NSP use by multivariate logistic regression.Of 700 eligible individuals interviewed, 657 provided information on their main source of equipment; 26% reported pharmacy NSP, 56% SMSNSP and 18% secondary distribution. In the adjusted analysis, individuals whose main source was SMSNSP were more likely to report markers of increased risk (homelessness, groin injection, having injected >16 days/month) and had a higher hepatitis B antibody prevalence than individuals primarily using pharmacy NSP. Individuals whose main source was secondary distribution had a different profile (e.g. they were younger, more likely to be recent onset injectors than main source SMSNSP users and less likely to report being in drug treatment).Differences exist in the populations primarily accessing different NSP and commissioning of services must reflect these differences. Injecting drug users relying on secondary exchange should be targeted to improve health service contact.