We conducted this study among HIV-infected injection drug users to determine the effect of self-reported alcohol use and prior incarceration at the time of initiating antiretroviral therapy on subsequent HIV-1 RNA suppression. We examined the demographics, recent incarceration history, and drug and alcohol use history from the Vancouver Injection Drug User Study (VIDUS) questionnaire closest to the date of initiating antiretroviral therapy. We linked these data to the HIV/AIDS Drug Treatment Program. There were 234 VIDUS participants who accessed antiretroviral therapy through the Drug Treatment Program from August 1, 1996, to July 31, 2001. In terms of illicit drug use, 196 (84%) reported injecting heroin and cocaine at the time of initiating antiretroviral therapy. Multiple logistic regression revealed that in the 6 months prior to initiating antiretroviral therapy, alcohol use (adjusted odds ratio [AOR] 0.32; 95% CI 0.13–0.81) and incarceration (AOR 0.22; 95% CI 0.09–0.58) were independently associated with lower odds of HIV-1 RNA suppression. Factors positively associated with HIV-1 RNA suppression included: adherence (AOR 1.27; 95% CI 1.06–1.51); lower baseline HIV-1 RNA (AOR 1.30: 95% CI 1.01–1.66); highly active antiretroviral therapy (AOR 4.10; 95% CI 1.56–10.6); months on therapy (AOR 1.1; 95% CI 1.06–1.14). Among HIV-infected injection drug users who were on antiretroviral therapy, any alcohol use and incarceration in the 6 months prior to initiating antiretroviral therapy were negatively associated with achieving HIV-1 RNA suppression. In addition to addition treatment for active heroin and cocaine use, the identification and treatment of alcohol problems should be supported in this setting. As well, increased outreach to HIV-infected drug users recently released from prison to ensure continuity of care needs to be further developed.