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The protozoon parasite Cryptosporidium is a pathogen that infects humans and animals. It causes cryptosporidiosis, which results in an acute or chronic diarrhea. The infectious agents of this parasite are oocysts, which are excreted into the environment with feces of the infect­ed host. Humans can become infected either directly through contact with infected humans and animals, or indirectly via contaminated water and food. In the absence of effective ther­apeutics against this parasite, preventing the infection is very important. The development of molecular biology-based techniques gave the insight into the extensive genetical variation within Cryptosporidium. In adition to the thirteen accepted species of Cryptosporidium, over thirty Cryptosporidium genotypes have been described. Thus far, seven species and one geno­type have been identified in humans. Molecular characterization of Cryptosporidium species/genotypes that infect humans in a certain area most frequently enables us to infer about the sources of infection and transmission routes of cryptosporidiosis in this area and to introduce appropriate intervention measures to prevent the infection. A molecular biol­ogy based technique was used in our laboratory to determine the species and genotypes of Cryptosporidium that infect humans in Slovenia.