Cryptosporidium an apicomplexan parasite has the ability to induce diarrhea in bovines, goats, pigs, dogs and cats worldwide. In this study, buffalo calves fecal samples were examined after staining their smears with Modified Ziehl-Neelsen Stain (MZN). Ileal sections were examined for the detection of pathological changes. Further molecular characterization was done using nested PCR amplification and partial sequence analysis. The detected oocysts were morphologically similar to Cryptosporidium parvum. Light microscopic examination of Cryptosporidium infected ileal Tissue Section (TS) stained with H and E revealed the presence of altered mucosal architecture with congestion of blood vessels, infiltration, sloughing and complete erosion of epithelial cells and shortening, blunting, stunting and atrophy of the intestinal villi. Molecular characterization gave PCR amplicons of 18S SSU rRNA gene products approximately at 823 bp. Sequences proved specified generalized relatedness with 21 species of Cryptosporidium but the nucleotide homogeneity percentage was insufficient to designate species or genotypes. Further bioinformatics analysis showed that resulting Cryptosporidium isolates had the closest match with three isolates. It was implied that the Cryptosporidium isolates is mostly like Cryptosporidium parvum (JX237832.1) previously isolated from buffaloes in Ismailia province.