Cryptosporidium parvum is a protozoan parasite responsible for a number of water-borne outbreaks of human gastrointestinal infection. The importance of this parasite for human health has led to several investigations into its epidemiology. In the present study, sequence and PCR-RFLP analyses were performed on cloned SSU rRNA genes from human and bovine C. parvum isolates. Each cloned gene was assigned a genotype using AseI restriction digestion profiles. Although sequence heterogeneity was observed, six of seven human isolates contained human genotype SSU rRNA genes and one human isolate contained bovine genotype genes. No intra-isolate variation was observed between the SSU rRNA genes analysed from a single bovine (Iowa) isolate. Intra-isolate variation did not occur at the Ase I restriction sites and therefore did not interfere with the assignment of C. parvum genotypes by RFLP. Mixed RFLP genotypes (human and bovine) were not observed in any of the C. parvum isolates analysed.