Background Frequent use of emergency rooms by injection drug users (IDUs) has been attributed to a lack of access to primary care and barriers to health services. Using a community-based sample of IDUs, we examined rates of primary care and emergency room use among IDUs and identified correlates of frequent emergency department use. Methods From January to November 2003, we enrolled IDUs into a prospective cohort study involving a baseline questionnaire, comprehensive retrospective and prospective health record linkages. We examined rates of primary care and emergency department utilization, and diagnoses upon arrival in the emergency room. Logistic regression was used to determine factors independently associated with frequent emergency room use. Results Of the 883 IDUs included in this analysis, 687 (78 per cent) accessed a primary care clinic in the previous year, while 528 (60 per cent) participants accessed the emergency room (ER) during the years 2002 and 2003. Abscesses, cellulitis and other skin infections accounted for the greatest proportion of ER use. Factors independently associated with frequent ER use included: frequent crystal methamphetamine injection (AOR = 2.4, 95 per cent CI: 1.0–5.6); non-fatal overdose (AOR = 2.1, 95 per cent CI: 1.4–3.3); HIV-positive status (AOR = 1.5, 95 per cent CI: 1.1–2.1), having been physically assaulted (AOR = 1.5, 95 per cent CI: 1.1–2.1); and primary care utilization (AOR = 1.5, 95 per cent CI: 1.0–2.1). Discussion High rates of ER use were observed among IDUs, despite high rates of primary care use among this same population. ER use was due primarily to preventable injection-related complications that are less amenable to primary care interventions, and therefore educational and prevention efforts that encourage and enable sterile injection practices should be promoted.