Cryptosporidium paruum has become one of the most important contaminant found in drinking water and is associated with high risk of waterborne diseases particularly for the immunocompromised. In the present study, Cryptosporidium was found in uncovered water tanks, nearby the shore in El Noubareya and El Mahmoudeya canals and in one swimming pool. Direct flourescence monoclonal antibody was more sensitive in detecting the organism. Ziehl-Neelsen although less sensitive, yet it has the advantage that it could recognize other protozoa causing diarrhoea as G. lamblia, B hominis and Cyclospora sp.