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Background: While dyslipidemia importantly contributes to increased cardiovascular disease risk among patients on antiretroviral therapy (ART), data on lipid patterns among African adults on ART are limited. We describe the prevalence of lipid abnormalities and associated factors in two HIV clinics in Malawi. Methods: We conducted a cross-sectional study in 2014 and enrolled adult patients at a rural and an urban HIV clinic in Zomba district, Malawi. We recorded patient characteristics, CVD risk factors and anthropometric measurements, using the WHO STEPS validated instrument. Non-fasting samples were taken for determination of total cholesterol (TC), triglyceride (TG) and HDL-cholesterol (HDL-c) levels. Logistic regression analysis was used to determine factors associated with elevated TC and elevated TC/HDL-c ratio. Results: 554 patients were enrolled, 50% at the rural HIV clinic, 72.7% were female, the median (IQR) age was 42 years (36–50); 97.3% were on ART, 84.4% on tenofovir/lamivudine/efavirenz, 17.5% were overweight/obese and 27.8%% had elevated waist/hip ratio. 15.5% had elevated TC, 15.9% reduced HDL-c, 28.7% had elevated TG and 3.8% had elevated TC/HDL-c ratio. Lipid abnormalities were similar in rural and urban patients. Women had significantly higher burden of elevated TC and TG whereas men had higher prevalence of reduced HDL-c. Waist-to-hip ratio was independently associated with elevated TC (aOR = 1.90; 95% CI: 1.17–3.10, p = 0.01) and elevated TC/HDL-c ratio (aOR = 3.50; 95% CI: 1.38–8.85, p = 0.008). Increasing age was independently associated with elevated TC level (aOR = 1.54, 95% CI 0.51–4.59 for age 31–45; aOR = 3.69, 95% CI 1.24–10.95 for age >45 years vs. ≤30 years; p-trend <0.01). Conclusions: We found a moderate burden of dyslipidemia among Malawian adults on ART, which was similar in rural and urban patients but differed significantly between men and women. High waist-hip ratio predicted elevated TC and elevated TC/HDL-c ratio and may be a practical tool for CVD risk indication in resource limited settings. [ABSTRACT FROM AUTHOR]