In the 3rd edition of its Guidelines for Drinking-Water Quality (2004) (GDWQ) the World Health Organization (WHO) promotes the use of risk assessment coupled with risk management for the control of water safety in drinking water supplies. Quantitative microbial risk assessment (QMRA) provides a tool for estimating the disease-burden from pathogenic microorganisms in water using information about the distribution and occurrence of the pathogen or an appropriate surrogate. This information may then be used to inform decisions about appropriate management of the water supply system. Although QMRA has been used to estimate disease burden from water supplies in developed countries, the method has not been evaluated in developing countries where relevant data may be scarce. In this paper, we describe a simplified risk assessment procedure to calculate the disease burden from three reference pathogens – pathogenic Escherichia coli, Cryptosporidium parvum and rotavirus – in water supplies in Kampala, Uganda. The study shows how QMRA can be used in countries with limited data, and that the outcome can provide valuable information for the management of water supplies.