A total of 30 fecal samples collected from individuals admitted to a local hospital in Nablus city in Palestine with gastroenteritis symptoms, plus 5 fecal samples from healthy individuals living in the same area were screened for the presence of Cryptosporidium spp. by microscopic analysis using malachite green negative staining. Molecular techniques were used to confirm the microscopic identification. Of these, all the 30 samples from individuals with gastroenteritis symptoms were positive by both techniques. No other parasites were found in the fecal material of patients or healthy individuals. To explore the source of the outbreak, water was collected from various reservoirs and springs which supply the city with drinking water. Al-Qaryoon water spring was also found to be contaminated with Cryptosporidium using both microscopic and molecular analysis. No other water resources was found to be contaminated. Genotyping analysis of Cryptosporidium oocysts using PCR-RFLP technique identified the parasite as C. parvum. This study is the first of its type in the country, and it reports the presence of cryptosporidiosis in the region.