Cryptosporidiosis a global health concern in large part because the causative organism, Cryptosporidium , is a ubiquitous water contaminant throughout the planet. Transcriptional analysis of the parasite has been limited to the pre-attachment stage, the sporozoite. This research describes the transcriptome of the attached C. parvum over a 72 hr in vitro infection utilizing real time PCR. These data provide direct insight into the parasite's biochemical requirements over its developmental life cycle. The parasite gene transcription is dependent upon the developmental stage present and stage specific gene predictions were deduced. Furthermore, a comparison of the gene transcription between C. parvum and C. hominis in duplicated infection protocols indicates that although these two species are almost identical at the nucleotide level, phosphorylation related genes are not expressed at concurrent time points. Additional promoter analysis indicates that genes with differing expression between these two species are more likely to contain a gap in the upstream sequence.