Unsafe sanitation systems poses a risk for pathogen transmission, wherefore it is important to both inactivate pathogens present in human excreta and conduct safe sanitation systems from use to end-use. The Peepoo toilet, using ammonia sanitisation, have been suggested as a low-cost sanitation solution and is implemented in schools in Kibera, an urban slum in Kenya. This master thesis aim to study the inactivation efficiency of ammonia sanitisation when treating human excreta with urea, and to quantify the risks of exposure to microbial hazards from the Peepoo sanitation system using faecal indicator bacteria. Excreta was collected from four schools in Kibera. After adding urea to mimic the inactivation of the Peepoo in the laboratory, the inactivation rate was correlated to temperature and free ammonia concentration for Campylobacter spp., Escherichia coli and Enterococcus spp.. Campylobacter spp. and E. coli both had a high inactivation rate even at low temperature and low addition of urea. Inactivation rate of Enterococcus spp. was lower and close to zero when 1.87 % urea was added for 15 °C. For Enterococcus spp. a lag-phase was observed, which was not affected by temperature but by concentration of free ammonia. For investigated bacteria, inactivation rate increased with increased temperature and free ammonia concentration. Along the Peepoo management chain, several hazardous events were identified such ascontamination during usage, handling and transportation. Sampling showed a higher contamination of Enterococcus spp. than of E. coli. Enterococcus spp. was used as a faecal indicator for Ascaris and E. coli was used as an indicator of E. coli O157:H7 in a quantitative microbial risk assessment (QMRA). Through the QMRA, the risk of infection of Ascaris and E. coli O157:H7 for one exposure event was simulated based on a Exponential and a Beta-Poisson dose-response model respectively. The risk of infection of Ascaris was around 12 % regardless of where exposure occurs, if Ascaris eggs were present. For risk for infection with E. coli O157, the simulated risks were below 10 % at almost all exposure points, with most of the high risk exposure points located in the schools. There are risks of pathogen transmission in the Peepoo management chain that should be further investigated. Ammonia sanitisation permits a high degree of microbial inactivation but to secure a safe end-product it is recommended to be kept in room temperature (24.05±0.62 °C) or higher.