Apicomplexan parasites are responsible for some of the most devastating human and veterinarian diseases and are parasites of great economic importance. Apicomplexa include Plasmodium, Toxoplasma and Babesia species. The pathogenic mechanisms developed by Apicomplexa parasites, in particular those that reside in a parasitophorous vacuole, involve considerable changes to the host cell, including the expression of variable surface proteins required for immune evasion. In Plasmodium falciparum infections, host cell remodeling is responsible for disease symptomology and severity in the human host. This work represents a multi-faceted study of antigenic secretion and the role of secreted antigens in pathogenesis. We study in detail the mechanisms of antigen secretion in Apicomplexa parasites. By use of comparative genomics, we find Plasmodium Export Element (PEXEL)-like motifs in a subset of Cryptosporidium and Babesia secreted proteins. However, in Babesia the motif functions as a spherical body targeting sequence, suggesting that secretory mechanisms in Apicomplexa are adapted to the parasite's intracellular lifestyle. To elucidate the relationship and function of exported antigens, we first focused on P. falciparum to determine gene co-expression modules. We found that in vivo, export modules are composed of constitutively or variably expressed genes, the latter group associated with patient clinical phenotypes. We then focused on a novel gene family called "phist" and show, using transcriptional expression profiling, its role in P. falciparum cytoadherence. In total, we demonstrate that antigen secretion is an evolutionary mechanism in Apicomplexa parasites and that variant expression of the genes encoding these antigens may allow parasites to adapt to environmental stresses.