Compost toilet systems were assessed for their ability to reduce microbial indicators and pathogens. Bacterial pathogens were not detected in any samples indicating a low survival rate in composting feces and/or an initial low occurrence. Indicator bacteria showed large variations with no clear trend of lower bacterial numbers after longer storage. In controlled composting experiments, thermophilic conditions were only reached when amendments were made (grass and a sugar solution). Even then it was impossible to ensure a homogenous temperature in the composting fecal material and therefore difficult to achieve a uniform reduction and killing of indicator organisms. Presumptive thermotolerant coliforms, Salmonella typhimurium Phage 28 B and eggs of Ascaridia galli, proved useful as indicators. However, regrowth was detected for enterococci and total numbers of bacteria grown at 36 degrees C. These indicator parameters may therefore overestimate the level of other (pathogenic) bacteria present in the material and can not be recommended for use as reliable indicator organisms in composting toilet systems. The addition of indicator bacteria to fecal material contained in semi-permeable capsules proved to be a useful technique to ensure that microorganisms were contained in a small test volume.