Available evidence suggests that a number of important clinical events in individuals with HIV infection are related to mitochondrial dysfunction. Several factors may contribute to the development of these events and the tissue(s) in which the event occurs. Some individuals are likely to have important genetic predispositions for mitochondrial disease, which may be unmasked by the presence of HIV infection or the introduction of NRTI antiretroviral drugs. HIV infection per se is associated with reduction in mtDNA content and changes in mitochondrial morphology and function, which in some cases leads to clinical events such as myopathy or distal symmetrical neuropathy. NRTI antiretroviral agents may impact mtDNA content and function through a number of different mechanisms and have been demonstrated to be causative of a number of clinical toxicities. A range of other clinical events occurring in individuals with HIV infection, and particularly those on therapy, have also been suggested to be associated with mitochondrial dysfunction. Newer nucleoside and nucleotides agents such as lamivudine, abacavir, and tenofovir appear in vitro and in limited clinical data to be less likely to inhibit mitochondrial DNA polymerase-γ or other mitochondrial functions and appear to be associated with a lower risk of events thought to be related to mitochondrial toxicity. Avoidance of mitochondrial toxicity is the better option. While drug choice plays an important role in the avoidance of mitochondrial toxicity, for many individuals treatment options are limited. Simple, non-invasive tests for mitochondrial function are not routinely available at present, and assays of mtDNA content in blood cells may miss key aspects of mitochondrial function, require careful sample handling and may not reflect events occurring in other tissues. There remains a need for the development of rapid, cheap and clinically applicable assays that would enable the prediction of increased likelihood of mitochondrial events. Additionally, international collaborative studies are required to look at interventions that may be used to enable individuals to remain on specific drug therapies but with a diminished risk of mitochondrial toxicity events.