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The present study aimed to determine the occurrence and removal of protozoan cysts and helminth eggs from municipal wastewater by pilot waste stabilisation ponds in the arid climate of Marrakech (Morocco). Protozoan cysts detected in raw wastewater at the entrance of the system were identified as Entamoeba histolytica, Giardia sp. and Entamoeba coli at a mean concentration of 1.5×104 cysts/l. Helminth eggs identified were Ascaris, Trichuris, Hymenolepis, Enterobius and Taenia with an average of 7.6 eggs/l. The effluent at the system outlet did not contain detectable cysts or eggs. Sludge samples collected in the pond basins resulted in detection of protozoan cysts and helminth eggs. Sedimentation therefore seems to be the main factor for cyst and egg elimination during wastewater treatment by waste stabilisation ponds. This phenomenon leads however to parasite accumulation in the sediment.