Polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) analysis of the Cryptosporidium parvum outer wall protein (COWP) gene was applied to specimens collected from 95 patients with cryptosporidiosis associated with two suspected waterborne outbreaks, 46 sporadic human cases and 62 infected livestock from other areas, and 12 patients infected with other gastrointestinal parasites. Ninety-six per cent of C. parvum isolates from patients linked to the two suspected waterborne outbreaks were of genotype 1; all the isolates from livestock were of genotype 2. Isolates from 59% of the sporadic human infections were of genotype 1 and 35% were of genotype 2. Specimens from two patients yielded both genotypes. Specimens from patients infected with other parasites yielded no amplicons.