To investigate Cryptosporidium infection among healthy people, we collected stool samples from 150 healthy individuals in Gokseong, Muan, and Imshil Counties, southwest Korea, where neighbors on both an animal farm and a river respectively. In 12 of 150 samples, Cryptosporidium oocysts were detected by means of modified acid-fast staining. The bovine genotype, Cryptosporidium parvum, was identified by PCR/RFLP and 18S rRNA sequencing. C. parvum existed endemically in these areas, and the residents showed a relatively higher infection rate for C. parvum than that for C. hominis. Our results indicate that countermeasures against Cryptosporidium infection must be taken in these areas to ensure human health.