The genus Cryptosporidium includes several species of intestinal parasites ofanimals and humans. Originally C. parvum was thought to be the only speciesinfecting humans, but recently new genotypes of unknown taxonomic status havebeen identified in rare cases. Current methods of detecting Cryptosporidiumoocysts in water, such as EPA methods 1622 and 1623, have significantly improvedrecoveries, but do not provide information on species or genotype. This paperdescribes the use of polymorphic microsatellites to characterizing waterborneoocysts. Microsatellites consist of a short repetitive sequence of motifs ofvariable length and have been applied in a multitude of fields where precisegenotyping is needed, such as forensic and clinical sciences. Because of the highlevel of length variability and ease of detection using conventional polymerasechain reaction (PCR), microsatellites are ideally suited for characterizingwaterborne oocysts. Includes 15 references, figures.