Apicomplexan parasites, including Plasmodium and Cryptosporidium, remain major causes of human and animal disease. The discovery of new vaccine candidates, antibody targets, and serological biomarkers requires access to large numbers of high-quality parasite proteins. However, many apicomplexan proteins are difficult to produce using conventional expression systems. Using the wheat germ cell-free system (WGCFS), we have established extensive protein and antibody resources for antigen discovery across apicomplexan parasites. Combined with high-throughput antibody profiling technologies, including AlphaScreen and bead-based assays, these resources have enabled the identification of vaccine candidates, targets of natural and vaccine-induced immunity, serological biomarkers, and mechanisms of antibody-mediated protection. I will present our recent work on Plasmodium and discuss how WGCFS-based antigen discovery is now being extended to Cryptosporidium species. Together, these studies demonstrate how WGCFS can accelerate antigen discovery across apicomplexan parasites.