Protozoa of the genus Cryptosporidium are associated with diarrhea in humans and animals worldwide. They are causative agents of acute, self-limiting gastroenteritis in immunocompetent individuals. In immunocompromised patients, the disease can be chronic and life-threatening. Infectious oocysts are transmitted through the faecal-oral route. Contaminated water sources are an important factor in large waterborne disease outbreaks. Multi-locus genotyping is the most informative tool for identifying sources of cryptosporidiosis and studying infection transmission. In this study, we analysed 73 DNA isolates from the faeces of 73 patients infected with Cryptosporidium parvum. Typing of C. parvum based on the multiple-locus variable number tandem repeat analysis (MLVA) was performed by determining the length of fragments of seven loci of the parasite genome: cgd1, cgd4, cgd8, MM19, MSF, cgd5 and cgd6. In 39/73 (53%) samples, the length of the fragments of all seven loci was successfully determined. In these 39 samples, 25 different multi-locus genotypes were identified. Twenty occurred only once and five appeared in more than one patient. Between 2010 and 2019, no outbreaks of cryptosporidiosis were confirmed in Slovenia. Cryptosporidium infections in Slovenia are mostly sporadic. Nevertheless, it appears that parasites isolated from the faeces of patients living in the same or a nearby geographical area may be genetically related.