Infection by the parasite Cryptosporidium is a leading cause of child mortality, no vaccine is available and the current drug treatment against this diarrheal pathogen is inefficient. The disease is transmitted through food or water contaminated with oocysts, the chlorine-resistant parasite stage. The parasite infects the epithelial cells of the small intestine in which it replicates intracellularly. Invasion and intracellular development require extensive modifications of the host cell that remain largely unknown at the molecular level. We recently showed that parasite secreted proteins play an important role in this process, however, our knowledge remains limited. Modifications of the enterocytes as well as persistent inflammation will alter the physiology of the gut and have long lasting impact on the children. We conducted a proteomic experiment, hyperLOPIT, on fractionated Cryptosporidium sporozoites to identify the content of the various secretory organelles. The characterization of Cryptosporidium virulence factors in combination with high resolution microscopy will help fill important gaps in our knowledge of the host/parasite interplay.