Cryptosporidium spp infections are recognized as important causes of diarrhoea in bothrnimmunocompromised and immunocompetent patients. Although a number of studies have beenrnconducted on the prevalence of intestinal parasites in Ethiopia, none of them had indicated thernimportance of cattle as reservoirs for the prevalent human cryptosporidiosis in Ethiopia. Inrnaddition, no study had molecularly characterized Cryptosporidium spp isolates to determine thernsource (reservior) of human cryptosporidiosis in Ethiopia. This study examined the prevalencernand distribution of cryptosporidiosis in 9 different locations in Ethiopia. 1034 human faecalrnsamples from patients with diarrhoea and 350 cattle dung were screened for Cryptosporidium spprnoocysts by using modified Ziehl-Neelson staining method. 79 human stool samples (7.6%) and 8rncattle (2.3%) were positive for Cryptosporidium spp. The highest prevalence in humans (10.6%)rnwas detected in the town of Awash 7 (Afar region) and the lowest prevalence (3.8%) in Bishofturntown (Oromia region). Molecular methods were used to determine genotypic and subgenotypicrndiversity of Cryptosporidium spp. isolates that infect humans in Ethiopia. DNA was extractedrnfrom all Cryptosporidium spp positive samples, PCR amplification of the Cryptosporidium spprnoocyst wall protein gene (COWP), small sub-unit ribosomal ribonucleaic acid (SSU-rRNA), andrn60 kilo-Dalton glycoprotein (GP60) gene fragments were performed. Genotype analysis by PCRRFLPrnbased on COWP and the SSU-rRNA genes, and subgenotyping by DNA sequence analysisrnof GP60 gene fragments showed the importance of cattle reservoir for the high prevalence ofrncryptosporidiosis in humans. 52% of the 79 human stool samples and 75% of 8 cattle dungrnsamples were positive in one or other of the three molecular characterization methods. Out of 79rnhuman stool samples, 21(26.6 %) yielded a SSU-rRNA PCR product; 30 (38 %) were positive forrnxivrnCOWP and 30 (38 %) were positive for GP60. The majority of isolates (95%) were identified asrnC. parvum, while only 2.5% were C. hominis and another 2.5% mixed infections of the twornspecies. Sequencing of the GP60 gene fragments of the 13 isolates resulted in three differentrnsubgenotypes of C. parvum, belonging to the zoonotic subgenotype family IIa, and one to thernsubgenotype of C. hominis (Ib). Phylogenetic analysis of the sequences showed C. parvumrnisolates to belong to three subgenotypes: 8 isolates typed as IIaA15G2R1; 3 isolates typed asrnIIaA16G2R1; and one isolate typed as IIaA16G1R1. The C. hominis genotype was typed asrnIbA9G3 subgenotype. The study has identified C. parvum as the major cause of humanrncryptosporidiosis in Ethiopia and has indicated the major source of cryptosporidiosis to bernzoonotic with some (limited) anthroponotic transmission of C. hominis. In addition, it wasrndetermined that antiretroviral treatment in HIV/AIDS patients reduces infection withrnCryptosporidium and other diarrheogenic protozoan parasites. Based on the findings of thernpresent study, creation of a central national database on the prevalence of humanrncryptosporidiosis would be a useful step, so that information could be pooled from differentrnregions of Ethiopia to better understand the epidemiology of the disease.rnKey words: Cryptosporidium, Epidemiology, Genotyping, Sequencing, zoonotic, anthroponotic,rnEthiopia