Vascular endothelial dysfunction may contribute to the increase in cardiovascular events during HIV-1 infection and its treatment. Antiretroviral therapy (ART), metabolic factors, lipodystrophy, and HIV infection itself may be involved. Ninety-six HIV-infected subjects were evaluated for endothelial function by measurement of brachial artery flow-mediated dilation (FMD) by ultrasound, single-slice CT of the abdomen and mid-thigh, wholebody dual x-ray absorptiomety (DXA) scans, and metabolic evaluations in a cross-sectional study. The median age was 40 years; 28% were female, 38% black, 3% Hispanic, and 59% white. Forty-nine (51%) were receiving ART, which included a PI in 28 (57%) and was non-PI based in 21 (43%). FMD (AESD) in subjects not on ART was 5.5 AE 4.3%, PI-ART 5.3 AE 3.6%, and non-PI-ART 5.5 AE 4.1% ( p ¼ 0.9). Age, race, CD4 cell count, and HIV RNA did not correlate significantly with FMD. Among ART-treated subjects in the lowest tertile of thigh subcutaneous fat area (range 3-31 cm 2 ), FMD was 4.4 AE 3.5% and in the highest tertile (range 67-237 cm 2 ) FMD was 6.8 AE 3.6% ( p ¼ 0.07, t-test). However, in multivariate analyses, no body composition measure showed a significant association with FMD for either the group as a whole or in ART-treated subjects. ART use, PI use, CD4 cell count, and HIV RNA levels were not associated with endothelial dysfunction by brachial FMD. A definitive association with measures of adiposity was not detected in multivariate analysis, suggesting that lipoatrophy may not be an important contributor to endothelial dysfunction in HIV-infected individuals on ART.