Introduction: The burden of kidney disease in sub-Saharan Africa is currently poorly understood. Very limited monitoring and treatment is available for people affected. The association with other diseases and with mortality is unknown in this setting. We sought to determine the association between kidney function and subsequent all-cause mortality. Methods: In a general population cohort with detailed measurement of health-related parameters in rural Uganda, we estimated the baseline glomerular filtration rate (GFR) between 2011-2014 in 5,678 participants. We followed participants up to March 2019 with regular ascertainment of mortality and migration. Using multivariable cox regression, we determined associations between baseline eGFR and mortality. Results: The median age of the participants at baseline was 36 years (IQR 24-50), 60.7% were female, 14.6% hypertensive, 9.7% HIV-positive and 1.8% diabetic. We registered 140 deaths with a median follow-up of 5.0 years. Adjusting for age and sex, HIV, hypertension, diabetes, BMI, marital status, and alcohol and tobacco use participants with eGFR ≤45 mls/min/1.73m2 had six-fold higher mortality compared to those with eGFR ≥90mls/min/1.73m2 (HR 6.12 (95% CI 2.27-16.45)) with strong evidence of a linear trend for risk of mortality as renal function declined (P<0.001). Conclusions: In a prospective cohort with high rates of follow-up we found that baseline kidney function was associated with subsequently increased mortality in a graded manner. Improved understanding of the determinants of kidney disease and its progression are needed in order to inform interventions for prevention and treatment.