Currently more than one billion people worldwide do not have access to safe drinking water or adequate sanitation. Important water-borne diarrhoeal diseases include cryptosporidiosis and giardiosis. Both in developed and developing countries, Cryptosporidium and Giardia are important causes of diarrhoea. This thesis aimed at studying (water-borne) transmission of Cryptosporidium and Giardia in Belgium and in Bangladesh. The literature review (chapter 1) starts with introducing Cryptosporidium and Giardia, followed by an overview of their prevalence and clinical importance in both human and animals. Then the different transmission cycles of both parasites are discussed, including water-borne transmission through drinking water and recreational water. Finally, different methods for detecting and quantifying Cryptosporidium and Giardia in water are described. In chapter 2, we monitored the presence of Cryptosporidium and Giardia in four drinking water catchment sites in Belgium. An attempt was made to determine the origin of (oo)cysts applying molecular tools. No contamination was found in purified drinking water at any site. In three catchments (Zillebeke, Gavers and Dikkebus), only low numbers of (oo)cysts were recovered from raw water samples. However, raw water samples from the Blankaart catchment site were frequently contaminated with Cryptosporidium and Giardia, especially in winter and spring. C. andersoni, C. suis, C. horse genotype, C. parvum and C. hominis and Giardia duodenalis assemblage AI, AII, BIV, BIV-like and E were identified. The genotyping results suggest that agriculture may be a more important source of surface water contamination than human waste in this catchment. Continuous monitoring of treated water for the presence of Cryptosporidium and Giardia would be justified and (point) sources of surface water contamination should be identified. In chapter 3, the infection risk of Cryptosporidium and Giardia in recreational waters in Belgium was assessed in swimming pools, recreational lakes, ...