Neonatal calves are prone to Cryptosporidium infection resulting in economic loss as well as a significant source for zoonotic infection. This study was devoted to ascertain the prevalence and molecular analysis of Cryptosporidium in dairy calves at Kafr El Sheikh Province, Egypt. Twenty-nine out of 96 faecal specimens collected from calves, less than 6 weeks of ages, microscopically showed cryptosporidia oocysts (prevalence 30.2%). Among 29 positives, 26 samples were clearly sequenced for the SSU rDNA gene and the Cryptosporidium oocyst wall protein gene (COWP). Homology search revealed that 2 samples were C. andersoni and 24 isolates were C. parvum genotype II. By sequence analysis of the high polymorphic 60-kDa glycoprotein gene, 23 samples of C. parvum belonged to the allele IId (subtypes IIdA20G1), and one sample belonged to the allele IIa (subtype IIaA15G2R1). Prevailing of allele family IId is a unique observation, contrasting the conception that IIa has been the most prevailing allele in calves and cattle generally in other countries such as in Europe and the USA. To our knowledge, this is the first molecular report about genotyping and subtyping of Cryptosporidium in Egypt.