The recombinant SA35 peptide has been described as an antigenic portion of a larger Cryptosporidium parvum protein. We identified and characterized the encoding Cpa135 gene and the entire protein, Cpa135. The Cpa135 gene was found to consist of a single exon of 4671 bp, and the mRNA transcribed in the sporozoites was identified. The predicted 1556 amino-acid protein showed the presence of domains which are widely conserved also in other unrelated phylogenetic groups (i.e. a ricin B and a LCCL motif). Comparison of Cpa135 sequence with genomic and protein databases revealed many related genes in other apicomplexan species and high homology with CCP2 protein from Plasmodium yoelii and Plasmodium berghei. The Cpa135 protein was identified and localized by using a monoclonal antibody (Mab) directed against the SA35 antigen (anti-SA35). In oocyst-sporozoite lysate, the anti-SA35 MAb recognized a 135 kDa protein that forms a protein complex larger than 200 kDa, which is mediated by disulfide bridges. Cpa135 synthesis was up-regulated during the excystation process. After host-cell invasion, Cpa135 gene expression was undetectable up to 48 h, whereas mRNA synthesis was newly observed at 72 h post-infection. The Cpa135 protein was localized in the apical complex, and it was found to be secreted by sporozoites during their gliding. Cpa135 persisted during the intracellular stages of the parasite, and it defined the boundaries of the parasitophorous vacuole in the infected cells. The unique array of domains and the homology with other apicomplexan proteins indicate that the Cpa135 protein is representative of a new family of proteins.