The objectives of this study were to evaluate anti-retroviral (ARV) prescription pickups during twelve months following the first prescription and to identify factors associated with irregular pickups or permanent dropout in two public HIV/AIDS referral centers in Belo Horizonte, Minas Gerais State, Brazil. Participants (n = 323) were antiretroviral naïve and were recruited from May 2001 to May 2002. A total of 98 (30.3%) patients abandoned treatment, and 187 (57.9%) had at least one irregular pickup. Patients with irregular pickups and dropouts were compared to those with regular pickups. Multinomial multivariate analysis showed that living outside Belo Horizonte, CD4+ T-lymphocyte count greater than 200/mm(3), and antiretroviral regimen without protease inhibitors were associated with irregular pickups. In addition to these variables, not being on other medications, and any non-adherence recorded on patient charts were associated with treatment dropout. Pharmacy records are important potential indicators of non-adherence and should be incorporated as such in clinical practice. Strategies should be prioritized to reach out to dropouts or patients with irregular ARV pickups.