Although the dramatic effect of highly active antiretroviral therapy (HAART) in reducing morbidity and mortality must not be underestimated, it is also important to consider the incidence and prevalence of HAART-related toxicities. Although several studies have investigated HAART-related toxicities, there has been great variety between them in the reported incidence and prevalence rates of these toxicities. Various factors, including whether the study type was a clinical trial or an observational study, the definition of the toxicity endpoints, the demographic characteristics of the study populations and the effect of calendar year on analyses, may all influence the rates observed. We investigated the possible explanations for the differences in the incidence and prevalence rates of HAART-related toxicities between studies, focussing on metabolic and hepatotoxic disorders.