AIM: Accurately estimating child mortality in rural communities in Africa with poor vital registration is a challenge. We aimed to estimate mortality rates and risk factors for children under five years old in rural Uganda. METHODS: Age-specific mortality rates were estimated using the synthetic cohort life-table technique for 10 118 children under the age of five years, between 2002 and 2012. Calendar year-specific hazard rates were calculated using five-year moving averages, and risk factors were explored by Cox regression. RESULTS: The mortality rate was 92 per 1000 newborn infants from birth to five years, based on a total of 256 deaths. It was 40 for boys and 23 for girls in the neonatal period and 68 for boys and 42 for girls up to the age of one year. A substantial decline in mortality from 2002 to 2012 was observed between the ages of 28 days and 11 months. Multivariate analysis demonstrated that mortality increased with decreasing child age, home delivery, human immuno-deficiency virus in the child, a birth interval of less than one year, having an unmarried mother and a maternal parity of more than four. CONCLUSION: Under-five mortality rates in rural Uganda are driven by maternal factors.