Cryptosporidiosis is a major diarrheal disease with high mortality, primarily in young animals, and a zoonotic risk of infection. The molecular epidemiology patterns of Cryptosporidium isolates are still poorly understood in Egypt and other developing countries. The goal of this research was to better understand the genetic diversity of Cryptosporidium isolates in pre-weaned cattle calves in Egypt's Al-Sharkia governorate by examining the hemo-biochemical changes in infected calves. We used 100 diarrheal faecal samples to detect the presence of Cryptosporidium oocysts by Ziehl-Neelsen (ZN) staining. Twenty-two of the positive samples after staining were further verified using PCR targeting the Cryptosporidium oocyst wall protein (COWP) gene. We found that Cryptosporidium. Parvum (C. parvum) was the sole species identified using the polymorphic 60 kDa glycoprotein gene (GP60) locus. Sequencing GP60 locus samples revealed dominant circulation for subtype IIa of C. parvum in calves, unlike most previously reported sequences in Egypt. These sequences were 100% like those in Latin America (Brazil, KT948746 EPC30). Egypt imports cattle calves from Latin America, mainly Brazil, to overcome the deficiency in meat production, so it is more likely that the C. parvum sequences circulating in Egypt appear to be from different origins. Red Blood Cells (RBCs), Hemoglobin (Hb), Mean Corpuscular Hb (MCH), lymphocytes, and Total Iron Binding Capacity (TIBC) values were all significantly diminished in the infected calves than in the healthy ones, while Packed Cell Volume (PCV) and Mean Corpuscular Volume (MCV), neutrophil, eosinophil and monocytic percentages, Aspartate (Asp), and Glutamate Decarboxylase (GAD) values increased. Our study for the first time identified the presence of C. parvum isolates and changes in hemato-biochemical conditions in pre-weaned cattle calves in Al-Sharkia governorate, which may address the potential role of imported livestock in disease transmission.