We conducted a retrospective cohort study using pharmacy records to assess the frequency of delay in picking up antiretroviral (ARV) medication refills from the pharmacy and to identify determinants of delay among HIV-infected patients at two Brazilian hospitals. We selected patients who were on ARV therapy before January 2001 at Nova Iguaçu Hospital (NIPRH) (N = 265) and Evandro Chagas (N=424) Clinical Research Institute. We abstracted medical records and pharmacy data using standardised forms and analysed potential associations between delay in refilling medications and patients' demographic characteristics, type of ARV drug regimen and evolution of HIV disease. Sixty-nine patients (26%) had delays in medication refills >1 month at least once in 2001 at NIPRH compared with 140 (33%) patients at IPEC (p=0.052). No factor was found to be associated with having a delay in medication refill >1 month at NIPRH. At IPEC, delays in medication refill >1 month were associated with a median CD4+ T cell count <200/mm(3) versus >500/mm(3) (adjusted odds ratio (AOR) = 3.8; 95% confidence interval (CI) =1.6-8.9) and with dual protease inhibitor-based ARV regimens versus other regimens (AOR = 4.3; 95% CI = 1.9-9.4). In conclusion, rates of delay in medication refills were similar to rates of adherence to ARV therapy found in other studies in Brazil, suggesting that delay in medication refills could be used as a surrogate for adherence. Analysing ARV medication refills can complement self-reported information on adherence.