Water contamination by Giardia lamblia and Cryptosporidium is one of the causes of diarrhoea throughout the world. A total of 161 and 84 samples were collected from Jeddah and Makkah cities, respectively. Each sample was concentrated by double centrifugation and the sediment was examined as a wet smear and after staining with Trichrome and Kinyoun stains. The results showed that 56 (35%) and 1 (0.62 %) samples of Jeddah were positive for the oocyst of Cryptosporidium and cyst of Giardia, whereas only 21 (25%) and 2 (2.4 %) samples of Makkah showed positivity for oocysts and cyst of these parasites. Overall Cryptosporidium contamination in bottled water and water from filling stations was 6.8% and 17.4%, respectively. Maximum contamination for Cryptosporidium was recorded in tap water which was 51% and 25% in Jeddah and Makkah, respectively