Chaperonin 60 (Cpn60) is a well-established marker protein for eukaryotic mitochondria and plastids. In order to determine whether the small double-membrane-bounded organelle posterior to the nucleus in the apicomplexan Cryptosporidium parvum is a mitochondrion, the Cpn60 gene of C. parvum sporozoites ( CpCpn60) was analyzed and antibodies were generated for localization of the peptide. Sequence and phylogenetic analyses indicated that CpCpn60 is a mitochondrial isotype and that antibodies against it localize to the rough endoplasmic reticulum-enveloped remnant organelle of C. parvum sporozoites. These data show this organelle is of mitochondrial origin.