Background: We compared biomarkers of vascular dysfunction among HIV-infected children to a demographically similar group of uninfected children and determined factors associated with these biomarkers. Methods and Results: We measured several biomarkers of vascular dysfunction: C-reactive protein (CRP), interleukin-6 (IL-6), and monocyte chemoattractant protein −1 (MCP-1) (inflammation); fibrinogen and P-selectin (coagulant dysfunction); soluble intracellular cell adhesion molecule-1 (sICAM), soluble vascular cell adhesion molecule-1 (sVCAM), and E-selectin (endothelial dysfunction); and leptin (metabolic dysfunction). Anthropometry, body composition, CD4%, HIV viral load, and antiretroviral therapy were recorded. Mean age was 14.8 years (106 HIV-infected children) and 12.3 years (55 control children). Sex and body mass index Z scores were similar. Infected children had higher sICAM, sVCAM, MCP-1, IL-6, and fibrinogen levels. E-selectin (P = 0.07), and CRP (P = 0.08) trended to be greater in the HIV group, yet leptin and P-selectin were similar. In multivariable analyses in the HIV-infected children alone, each 1 standard deviation increase in waist to hip ratio was associated with increases in sICAM (17%), MCP-1 (19%), IL6 (18%), and CRP (59%). CD4% was inversely associated with sVCAM, MCP-1, IL6, fibrinogen, and CRP. Conclusions: HIV-infected children have higher levels of biomarkers of vascular dysfunction than healthy children. Risk factors associated with these biomarkers include higher waist to hip ratios and HIV disease severity.