HIV-associated lipodystrophy, arising as a result of long-term therapy with antiretroviral medications, is a complex syndrome characterized by changes in regional fat mass, dyslipidemia, and insulin sensitivity that, once established, is difficult to reverse. The syndrome arises largely as a result of effects of nucleoside reverse transcriptase inhibitors and protease inhibitors on lipid metabolism. Many of these effects have their basis at a molecular level with nucleoside reverse transcriptase inhibitors linked to inhibition of mitochondrial RNA transcription, depletion of mitochondrial DNA and mitochondrial dysfunction and protease inhibitors linked with adipocyte toxicity through interference with the function of essential cellular transcription factors such as sterol regulatory element binding protein 1c. These molecular toxicities can affect non-adipose tissues, and together with secondary effects on lipid and glucose metabolism of changes in body fat mass, help to contribute to the dyslipidemia and insulin resistance characteristic of this syndrome. This review will summarize what is known of the molecular mechanisms underlying HIV-associated lipodystrophy. A greater understanding of these mechanisms is essential if effective therapeutic options are to be found.