Cryptosporidiosis is an important apicomplexan disease with medical and veterinary significance. There is still no effective drug for its control. Mitochondrion is an organelle which contains most protein and enzyme in eukaryotes, so the mitochondrion of Cryptosporidium may be a potential target of drugs. Recent studies provided evidence for a mitochondrial derived compartment in this parasite. But the organelle has some difference to that of other apicomplexan parasites. This organelle appears to lack its genome, and thus must be entirely dependent on nuclear-encoded proteins. This article reviews the evidence for the organelle in Cryptosporidium and its probable function.