The occurrence of Cryptosporidium and Giardia in indoor swimming pools in the Netherlands was studied at five locations. The backwash water from seven pool filters was analysed for the presence of Cryptosporidium oocysts and Giardia cysts for a period of 1 year. Of the 153 samples of filter backwash water analysed, 18 (11.8%) were found positive for either Cryptosporidium (4.6%), Giardia (5.9%) or both (1.3%). Oocysts and cysts were also detected in the water of one toddler pool and one learner pool. Although most of the (oo)cysts in the filter backwash water were dead, viable and potentially infectious oocysts were detected in the learner pool. On the basis of numbers of potentially infectious (oo)cysts detected in the learner pool, and assuming one visit to an infected pool per year, risk assessment indicated an estimated risk of infection with Cryptosporidium that exceeded the generally accepted risk of one infection per 10,000 persons per year. Guidelines for pool operators on how to manage faecal accidents and public information on the importance of hygiene in swimming pool complexes are recommended tools in controlling the risk of infection.