BACKGROUND: Dyslipidemia is a leading risk factor for atherosclerotic cardiovascular disease. There are few published epidemiological data regarding dyslipidemia in Africa. We determined full lipid and apolipoprotein profiles and investigated factors associated with lipid levels in urban and rural populations of north-western Tanzania and southern Uganda. METHODS: We conducted a cross-sectional survey of randomly-selected, community-dwelling adults (≥18yrs) including five strata per country: one municipality, two district towns and two rural areas. Participants were interviewed and examined using the World Health Organization STEPwise survey questionnaire. Serum levels of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, and apolipoproteins were measured. Factors associated with mean lipid levels were assessed by multivariable linear regression. Framingham 10-year cardiovascular risk scores were calculated with and without lipids. RESULTS: One-third of adults in the study population had dyslipidemia. Low high-density lipoprotein cholesterol affected 32-45% of rural adults. High total cholesterol, low-density lipoprotein cholesterol, and apolipoprotein B were found in <15% of adult population in all strata, but were more common in urban adults. Factors independently associated with higher mean low-density lipoprotein cholesterol and apolipoprotein B were female gender, older age, higher education, higher income, obesity, and hypertension. Framingham cardiovascular risk scores with and without lipids yielded similar results and 90% of study subjects in all strata were classified as "low risk". Among older adults (>55 years), 30% were classified as "high" or "very high" risk. CONCLUSIONS: Dyslipidemias are common among adults in north-western Tanzania and southern Uganda affecting one third of adult population. Overall, cardiovascular risk scores are low but high risk scores are common with older adults. Health services designed and equipped to diagnose and treat dyslipidemia are urgently needed.