BACKGROUND:: Successful conduct of HIV vaccine efficacy trials entails identification and enrollment of at-risk populations, assessment of appropriate end points as measures of vaccine efficacy for prevention of HIV acquisition, and amelioration of disease course among infected vaccinees, as well as identification of potential confounders or effect modifiers. Although not invariably useful and bringing their own cost in terms of measurement and validation, a variety of biomarkers may aid at each stage of trial conduct. METHODS:: A review of selected articles, chosen based on quality, relevance of the biomarker to HIV vaccine trials, and availability of the publication, was conducted. The authors also drew experience from current trials and other planned or ongoing trials. CONCLUSIONS:: Biomarkers are available to assess HIV incidence in potential study populations, but care is needed in interpreting results of these assays. During trial conduct, sexually transmitted infections such as herpes simplex virus type 2 may act as effect modifiers on primary and secondary end points, including HIV incidence and set point viral load. The utility of sexually transmitted infection biomarkers will likely depend heavily on local epidemiology at clinical trial sites. Analyses from recent large HIV vaccine efficacy trials point to the complexities in interpreting trial results and underscore the potential utility of biomarkers in evaluating confounding and effect modification. Copyright © 2009 by Lippincott Williams & Wilkins.