The lack of an adequate system for the in vitro cultivation of Cryptosporidium spp. has forced researchers to work on infected feces or tissues. Molecular and immunological analyses of Cryptosporidium stages must be preceded by complex preparatory steps involving the concentration, storage, purification, excystation of oocysts, and purification of sporozoites. This paper describes two new procedures for the purification of Cryptosporidium. The first, consisting of pretreatment of oocysts with sodium hypochlorite followed by concentration using a Percoll gradient, is suitable for nucleic acid analyses. The second, a concentration of untreated oocysts using a Cesium chloride gradient, is suitable for biochemical and immunological studies, but requires “fresh” oocysts.