This study has been conducted to estimate the occurrence of Cryptosporidium oocysts in water supplies in the Metropolitan area of Seoul, South Korea, for 10 years from 2000 to 2009. Water samples were collected quarterly at 6 intakes in the Han River and its largest stream and 6 conventional Water Treatment Plants (WTPs) serving drinking water for 10 million people of Seoul. Cryptosporidium oocysts were found in 22.5% of intake water samples and arithmetic mean was 0.65 oocysts/10 L (range 0-22 oocysts/10 L). Although the annual mean of oocyst number was as low as 0.04-1.90 oocysts/10 L, 3 peaks in 2004 and 2007 were observed and the pollution level was a little higher in winter. The lowest density was observed at Paldang intake and the pollution level increased at Kuui and Jayang intakes. At the end of the largest stream, oocysts were found in 70% of collected samples (mean 5.71 oocysts/10 L) and it seemed that its joining the Han River resulted in the increase at Kuui intake and downstream. Oocyst removal by physical process exceeded 2.0-2.3 log and then all finished water samples collected at 6 WTPs were negative for Cryptosporidium in each 100 L sample for 10 years. These results suggested that domestic wastewater from the urban region could be a source of Cryptosporidium pollution and separating sewage systems adjacent to the intakes could be meaningful for some intakes having weakness related to parasitological water quality.