Objectives While patients with HIV infection have an elevated stroke risk, ultrasound studies of carotid artery wall thickness have reported variable results. We hypothesized that subjects with HIV infection on chronic highly active antiretroviral therapy (HAART) would have increased carotid artery wall thickness by magnetic resonance imaging (MRI). Methods This cross-sectional study compared carotid artery wall thickness between 26 individuals infected with HIV on chronic HAART and 20 controls, without HIV infection but with similar cardiovascular risk factors, using 3.0-T noncontrast MRI. Inclusion criteria included male gender, age 35–55 years, and chronic HAART (≥3 years) among HIV-seropositive subjects; those with known cardiovascular disease or diabetes were excluded. Results Between subjects with HIV infection and controls, there were no differences in mean (± SD) age (47.8 ± 5.0 vs. 47.8 ± 4.7 years, respectively; P = 0.19) or cardiovascular risk factors (P > 0.05 for each). Mean (± SD) wall thickness was increased in those with HIV infection vs. controls for the left (0.88 ± 0.08 vs. 0.83 ± 0.08 mm, respectively; P = 0.03) and right (0.90 ± 0.10 vs. 0.85 ± 0.07 mm, respectively; P = 0.046) common carotid arteries. Among individuals with HIV infection, variables associated with increased mean carotid artery wall thickness included lipoaccumulation [+0.09 mm; 95% confidence interval (CI) 0.03–0.14 mm; P = 0.003], Framingham risk score ≥5% (+0.07 mm; 95% CI 0.01–0.12; P = 0.02 mm), and increased duration of protease inhibitor therapy (+0.03 mm per 5 years; 95% CI 0.01–0.06 mm; P = 0.02). Conclusions Individuals with HIV infection on chronic HAART had increased carotid artery wall thickness as compared to similar controls. In subjects with HIV infection, the presence of lipoaccumulation and longer duration of protease inhibitor therapy were associated with greater wall thickness.