Mitochondrial toxicity contributes to serious adverse effects observed in HIV-infected individuals treated with nucleoside reverse transcriptase inhibitors (NRTIs). However, similar mitochondrial abnormalities have recently been found even in treatment-naive patients, suggesting that chronic HIV per se could contribute to the toxicity observed in NRTI-exposed individuals. This review gives a current status of the field, with particular focus on recent observations suggesting that distinct mechanisms might cause such toxicity in both NRTI-exposed individuals and those naive to antiretroviral treatment.