Introduction: The protozoan parasite, Cryptosporidium Spp., widely spreads in both raw and drinking waters. It is the causative agents of waterborne diarrhea and gastroenteritis in the world. In the present study, a molecular assay was used for the detection and quantification of Cryptosporidium oocysts in environmental water samples.

Materials and methods: Thirty surface water samples were collected from Rasht City rivers and lagoons during 2009-2010. The samples were analysed for Cryptosporidium oocysts using Real Time PCR method. Samples were filtrated through a 1.2µm pore size cellulose nitrate membrane filter and then purified and quantified by Real-time PCR technique.

Results: Cryptosporidium oocysts were found in 19 of 30 the samples. Oocyst concentration was ranging from 0.007 to 27 oocysts per liter of the examined waters.

Conclusion: The present study showed that the investigated water supplies were contaminated by Cryptosporidium oocyst. This study indicated that in this level of oocysts there is a potential risk of waterborne cryptosporidiosis due to direct or indirect consumption of these waters by humans and animals. Real-time PCR is a technique that provides high sensitivity for detection quantitative purposes.