We compared multiple pharmacy refill-based adherence indicators for antiretroviral therapy, as well as thresholds for defining non-adherent behavior, based on ability to predict virological failure. A total of 29,937 pharmacy visits with corresponding viral load assessments were contributed by 8,695 patients attending a large clinic in Johannesburg, South Africa. Indicators based on pill coverage and timing of refill pickup performed comparably using the strictest thresholds for adherence [100 % pill coverage: odds ratio (OR) (95 % confidence interval (CI)) : 1.26 (1.15, 1.39); prescription picked up on or before scheduled refill date: 1.27 (1.16,1.38)]. For both types of indicators, the association between non-adherence and virological failure increased as the threshold defining adherent behavior was lowered. All measures demonstrated high specificity (range 84-98 %), but low sensitivity (5-19 %). In this setting, patients identified as non-adherent using pharmacy-based indicators are likely correctly classified and in need of interventions to improve compliance. Pharmacy based measures alone, however, are inadequate for identifying most cases of nonadherence.