Objective. To determine if fat distribution is altered in HIV-infected men without clinical evidence of lipodystrophy. Methods. In a cross-sectional design, 14 protease inhibitor (PI)-treated men with lipodystrophy and 12 PI-treated and five PI-naive men without clinical evidence of lipodystrophy underwent body composition and fat distribution analysis by dual-energy X-ray absorptiometry and computed tomography. Their fat distribution was compared to 43 uninfected male controls matched for age and BMI. Results. The percent of body fat in the trunk of men with HIV lipodystrophy was significantly greater compared to both HIV-infected and healthy controls. The percentage of body fat in the extremities was significantly lower in men with HIV lipodystrophy compared to both HIV-infected and healthy controls. HIV-infected men without clinical evidence of lipodystrophy also had a significantly greater percentage of total body fat in the trunk and a significantly lower percent of body fat in the extremities compared to healthy controls. Among the HIV-infected men, age was an independent predictor of truncal and extremity adiposity. Conclusion. This study suggests that a continuum of change is present in the adipose organ of HIV-infected men on antiretroviral therapy. Physical examination alone can miss significant changes in body fat distribution in HIV-infected patients.