BACKGROUND: Data on the burden of dysglycemia among HIV-infected patients on antiretroviral therapy (ART) in Africa are limited. We determined the prevalence of pre-diabetes and diabetes among HIV-infected patients who started ART when malnourished 2 to 3 years previously and investigated the association of dysglycemia with body composition. METHODS: Malnourished (body mass index (BMI) < 18.5 kg/m2) HIV-infected patients who were enrolled in the Nutritional Support for Africans Starting Antiretroviral Therapy (NUSTART) trial from 2011 to 2013 were followed-up from March to August 2015. Anthropometric, fat mass and fat-free mass by bioelectrical impedance, and C-reactive protein (CRP) data were collected at baseline and follow-up. At follow-up, we defined fasting glucose of 6.1-6.9 mmol/L as impaired fasting glucose (IFG) and 2-h oral glucose tolerance test (OGTT) glucose of ≥7.8 to <11.1 mmol/L as impaired glucose tolerance (IGT). Both of these were considered pre-diabetes. Fasting glucose of ≥7.0 mmol/L or impaired glucose tolerance of ≥11.1 mmol/L was defined as diabetes mellitus. The relation of pre-diabetes and diabetes with body composition was assessed using logistic regression. RESULTS: Two hundred seventy-three (57%) of 478 patients who were alive at trial conclusion were followed-up. The mean age was 41.5 (SD 9.8) years and 65.2% (178) were females. The mean follow-up BMI was 19.9 (SD 2.8) kg/m2, 12 (4.4%) were either overweight or obese, and 61 (22.3%) patients had pre-diabetes or diabetes. In multiple regression, upper tertiles of baseline hip circumference (OR: 0.41, 95% CI: 0.2, 0.8) and fat mass index (OR: 0.20 (0.1, 0.5), and upper tertiles of follow-up waist circumference (OR: 0.22 (0.1, 0.5), BMI (OR: 0.32 (0.1, 0.7), fat mass index (OR: 0.19 (0.1, 0.5) and the middle tertile of follow-up fat-free mass (OR: 0.36, 95% CI: 0.1, 0.8) were associated with lower risk of pre-diabetes and diabetes (P < 0.05 for all). Baseline and follow-up CRP were not predictors. CONCLUSIONS: Low rather than high measures of adipose tissue were associated with increased risk of pre-diabetes and diabetes. Additional studies are needed to further investigate the role of body composition and control of glucose metabolism in the pathogenesis of diabetes among persons living with HIV in Africa.