HIV protease inhibitors have been successfully incorporated into therapy for patients with HIV. These otherwise efficacious treatments present with multiple metabolic side-effects and body habitus changes known as the lipodystrophy syndrome. Direct associations of the lipid abnormalities with protease inhibitor use have been described, and ongoing studies are focused on describing mechanisms for future intervention. Mechanisms based on the molecular identity of the protease inhibitor target with human proteins, interference with aspects critical to lipoprotein production, and interference with adipocyte differentiation have been described. This review highlights the complexities of this syndrome, and discusses putative mechanisms whereby protease inhibitors cause hyperlipidemia.