The process of invasion by apicomplexan parasites is a carefully coordinated process involving the regulated release of specialized secretory organelles. Several lines of evidence suggest that proteases are critical for the assembly and trafficking of organellar content proteins. Further, invasion is accompanied by cleavage and shedding of secreted proteins as host cell invasion occurs. Recent studies in Toxoplasma gondii and other Apicomplexa have led to the identification of proteases that may mediate these processing events. Among these are subtilases, subtilisin-like serine proteinases that have essential roles in processing of secreted proteins in prokaryotes and eukaryotes. Other studies suggest that cysteine proteinases or rhomboid proteases, a newly described class of serine proteinases, may be important. In addition to providing insights into the invasion process, characterization of invasion proteases may lead to identification of novel targets for antiparasitic chemotherapy.