Introduction Non-communicable diseases (NCDs) are rapidly becoming leading causes of morbidity and death in low- and middle-income countries, including those in sub-Saharan Africa. Yet, the magnitude and distribution of established and emerging risk factors for NCDs have not been fully studied in sub-Saharan African countries in a large scale epidemiological context.

Methods We will carry out a cross-sectional population-based survey of cardiometabolic risk factors and disease of approximately 8 000 participants ages 13 years and older, in a rural population in Uganda. Trained field staff will conduct a questionnaire based upon the WHO STEPwise approach to Surveillance questionnaire; perform biophysical measurement, including anthropometry and blood pressure readings; and collect blood samples for biochemical analysis for cardiometabolic risk factors and infection.

Results By August 2011, data on approximately 6000 participants will have been collected. We will report initial findings, including the prevalence and distribution of lifestyle risk factors, physical measurements and biochemical measurements. Lifestyle risk factors will include tobacco use, alcohol consumption, diet and physical activity. Physical measurements will include blood pressure, body mass index and waist hip ratio, as indicators of hypertension and obesity, respectively. Biochemical measurements will include liver function tests, lipid levels and HbA1c as an indication of diabetes. Age and sex specific estimates will be reported.

Conclusion Population based epidemiological studies can provide reliable data on disease burden and their risk factors to help inform public health policy and programmes aimed at addressing the rise in NCDs in Uganda.