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With the advent of highly active antiretroviral therapy (HAART), dramatic improvements have been made in the quality and length of life in people living with HIV/AIDS (PLWA). Complications that are seen with increasing frequency in this group include venous thromboembolism events (VTE) and cardiovascular disease. Recent epidemiologic studies suggest PLWA have a 2-fold to 10-fold greater risk of VTE compared with age-matched controls. Several mechanisms associated with HIV infection, coupled with traditional risk factors, including age, opportunistic infections, and lifestyle choices, may contribute to a heightened risk of VTE and cardiovascular disease. It has been challenging to discern which of these complications are related to HAART. Herein, we review the risk of VTE in the pre-HAART and current HAART era. We call attention to particular instances where components of HAART have been associated with acute myocardial infarction, noncirrhotic portal hypertension and portal vein thrombosis. We also highlight potential drug–drug interactions between HAART and anticoagulant therapy. Additional studies are needed to better understand the mechanisms and risks associated with long-term use of HAART and to what extent HAART contributes to or mitigates the risk of VTE and cardiovascular disease.