A decade after widespread recognition that adherence to medication regimens is key to antiretroviral effectiveness, considerable controversy remains regarding a "gold standard" for adherence measurement. Each adherence measurement approach has strengths and weaknesses and each rests on specific assumptions. The range of assumptions regarding adherence measurement and the diversity with which each approach is implemented strongly suggest that the evaluation of a particular measure outside of the context in which it was used (e.g. the study's operational protocol) may result in undeserved confidence or lack of confidence in study results. The purpose of this paper is to propose a set of best practices across commonly used measurement methods. Recommendations regarding what information should be included in published reports regarding how adherence was measured are provided to promote improvement in the quality of measurement of medication adherence in research.