Background Following a HIV outbreak among Aboriginal people in a culturally diverse inner-city suburb of Melbourne, a blood-borne virus (BBV) screening program was conducted to inform public health interventions to prevent transmission and facilitate timely diagnosis and linkage to care. Methods: In August–September 2014, community health workers recruited people who inject drugs (PWID) from a local needle and syringe program. Participants were tested for hepatitis C virus (HCV), hepatitis B virus (HBV), HIV and syphilis and completed a bio-behavioural questionnaire. Results: In total, 128 PWID participated in the study. Serological evidence of exposure to HCV and HBV was detected among 118 (93%) and 57 participants (45%) respectively. Five participants were HIV positive. Independent risk factors for needle sharing were Aboriginality (AOR = 6.21, P < 0.001), attending health care for mental health problems (AOR = 2.79, P = 0.023) and inability to access drug treatment in the previous 6 months (AOR = 4.34, P = 0.023). Conclusions: BBV prevalence in this sample was much higher than reported in other recent Australian studies. This local population is at high risk of further BBV transmission, particularly Aboriginal PWID. Individual and service-related factors associated with risk in the context of a dynamic urban drug culture and HIV outbreak suggest an urgent need for tailored harm-reduction measures.