The phylum Apicomplexa consists of ~5000 species of parasitic protists. Many of these parasites are of great social and economic importance, including those responsible for malaria (genus Plasmodium), cryptosporidiosis (genus Cryptosporidium) toxoplasmosis (Toxoplasma gondii) and a number of other significant human and veterinary diseases. As such, many apicomplexan genomes have been sequenced to date. This dissertation describes our work to use these genomes to develop improved malaria diagnostic assays, as well as to study transcriptional regulatory phenomena in an organism with few experimental tools, Cryptosporidium parvum. We have shown that malaria diagnostic assays developed to conserved, repetitive sequences in several human-infecting malaria parasite genomes are species-specific and more sensitive than existing molecular diagnostics. We also present the first comprehensive study of a major transcription factor family in Cryptosporidium parvum, the ApiAP2s, and present evidence that C. parvum may not be as reliant on ApiAP2 regulation as previous research has indicated for other apicomplexans.