The concentrations of Cryptosporidium in the source water of several cities of Zhejiang Province, China were determined to be in the range of 0-17 oocysts/10 L in the rainy season in 2008, with a mean value of 7 oocysts/10 L. Based on the investigation data, comprehensive risk assessment of Cryptosporidium infection was performed by considering different water intake routes as well as water consumption. Intakes of unboiled tapwater (including drinking and tooth-brushing and food and dish washing) and source water (through swimming in rivers) were estimated to be 2.59-25.9 and 0.32-0.74 L/year-person, respectively. The mortality due to Cryptosporidium infection for people in this region, excluding HIV-infected patients, was calculated as 0-0.0146 per 10(5) persons using a conditional probability formula. Disability-adjusted life years (DALYs) were used to quantify the risk of Cryptosporidium infection, for which uncertainty was analyzed. For people who consumed conventionally treated water, the DALYs due to Cryptosporidium infection were 6.51 per 10(5) (95% CI: 2.16 × 10(-5)-22.35 × 10(-5)) persons, which were higher than a risk judged acceptable by some (1.97 × 10(-5) DALYs per year), and the risk for those consuming ozone-treated water became 0.0689 × 10(-5) DALYs per year. The major risk of infection resulted from swimming in the river. This study provides a method to establish the risk of Cryptosporidium infection and optimize the scheme for reducing the risk effectively, which is useful for the modification of water quality standards based on cost utility analysis given use of DALYs.