Procurement of sterile needles is an important intervention for reducing the transmission of blood-borne pathogens among injection drug users (IDUs). In San Diego, a syringe exchange program (SEP) is available; however accessibility to other safe syringe sources is limited because nonprescription sales of sterile syringes remains illegal. The aims of this study were to (1) estimate the proportion of IDUs in San Diego who are accessing SEP, other safe sources, or unsafe sources as their primary source for needles and (2) identify sociodemographic characteristics, injection practices, and other behaviors correlated with each of these primary syringe sources. From 2009 to 2010, a cross-sectional survey was administered to current drug injectors recruited through the SEP, street outreach, and recruitment driven sampling in San Diego, California. Data were collected with audio-computer assisted interview (ACASI) technology. Polychotomous logistic regression was performed to identify differences in characteristics of IDUs in San Diego primarily accessing the SEP, other safe, and unsafe syringe sources. Of 566 eligible individuals who completed the participant questionnaire, 529 provided information on their primary syringe source in the last three months; 58% reported unsafe sources, 29% reported SEP, and 13% reported other safe sources. After adjusting for recruitment method and other variables in the model, SEP users were more likely to inject everyday, use heroin (alone or with other drugs) as the drug they injected most frequently, inject with a new syringe at least half the time, report ease with obtaining new syringes, and ever been in drug treatment compared to IDUs who primarily used unsafe syringe sources. SEP users were also more likely to inject everyday compared to users of other safe syringe sources. The majority of IDUs in this study are still using unsafe sources to obtain syringes, suggesting the importance of improving sterile syringe access. Differences in injection practices by primary syringe source exist in IDU populations in San Diego. Interventions must tailor their programs and local policies must change to reflect these differences and to increase access to sterile syringes.