Background: Kidney disease is an important cause of morbidity and mortality globally. However, there are limited data on the prevalence of impaired kidney function in sub-Saharan Africa. We aimed to determine the prevalence of reduced kidney function and associated factors in a rural Ugandan population. Methods: We undertook a study of a representative sample of the General Population Cohort in South-western Uganda. We systematically collected data on cardiovascular disease risk factors, anthropometric measurements and blood tests including haemoglobin, HIV, HbA1c and serum creatinine. The estimated glomerular filtration rate (eGFR) was calculated using the CKD-Epi equation, without the race component of the equation. Results: A total of 5,979/6,397 (93.5%) participants had valid creatinine results. The mean age was 39 years (Range:16-103 years) and 3,627 (60.7%) were female. HIV prevalence was 9.7% and about 40% of the population were pre-hypertensive or hypertensive. The mean serum creatinine level was 0.75 mg/dl (95% CI 0.74–0.75), and the average eGFR was 109.3 ml/min/1.73 m 2 (95% CI 108.8–109.9). The overall prevalence of eGFR <60 ml/min/1.73 m2 was 1.64% (98/5,979) (95% CI 1.34–1.99). Additionally, 4,792(80.2%) were classified as normal eGFR (≥90 ml/min/1.73 m2), 1,089(18.2%) as low eGFR (60–89 ml/min/1.73 m2), 91(1.52%) as moderately reduced eGFR (30–59 ml/min/1.73 m2), 4(0.07%) as severely reduced eGFR (15-29 ml/min/1.73 m2), and 3(0.05%) classified as having kidney failure (eGFR<15 ml/min/1.73 m2). When age-standardised to the WHO Standard Population the prevalence of eGFR<60 ml/min/1.73 m2 was 1.79%. Age above 35 years and the presence of hypertension (OR 2.86, 95% CI 1.15-7.08) and anaemia (OR 2.14, 95% CI 1.12-4.09) were associated with eGFR<60 ml/min/1.73 m2. Conclusion: In a systematic survey of people in rural Uganda, we found a substantial proportion had eGFR<60 ml/min/1.73 m2. More population based studies are needed to further characterize kidney disease in sub-Saharan Africa.