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Cryptosporidium spp., Giardia duodenalis , Cyclospora cayetanensis , and Enterocytozoon bieneusi are known etiological agents of self-limiting diarrhea, chronic disorders, and severe debilitating illnesses in humans, particularly children and patients with immunodeficiency diseases. To assess the pathogen carriage status of raw vegetables and fruits and the potential transmission routes of the aforementioned parasites in Henan province, China, a total of 1099 vegetables and fruits samples (21 items) were purchased and collected from agricultural farms or open markets. Cryptosporidium spp., E. bieneusi , C. cayetanensis and G. duodenalis were screened by employing polymerase chain reaction (PCR) amplification of species-specific genes. Three kinds of human pathogenic agent (E. bieneusi , C. cayetanensis and C. parvum) were identified on the surfaces of the vegetables and fruits (3.7%, 41/1099). E. bieneusi was found in 3.5% (38/1099) of the samples, whereas C. cayetanensis and C. parvum were only identified in two (0.2%) and one (0.1%) of the vegetable and fruit samples, respectively. No G. duodenalis contamination was detected in the present study. In total, 12 different E. bieneusi ITS genotypes (eight known and four novel) were detected, of which the ten (EbpA, CM8, CHG19, EbpC, CTS3, Henan-IV, and CHV1 to CHV4) that occurred in 20 samples (20/38, 52.6%) clustered into the previously described high potential zoonotic group 1 in the phylogenetic analysis. The remaining two known genotypes (BEB8 and CD6) detected in 18 samples (18/38, 47.4%) belonged to group 2. That C. cayetanensis , C. parvum and some E. bieneusi genotypes have been reported in humans, highlights the possible risk of foodborne related disease outbreaks. • Three types of protozoan were identified on surface of vegetables and fruits. • These pathogens had previously been reported in human and animals stool. • A risk of parasitic illnesses associated with fresh fruits and vegetables consumption. [ABSTRACT FROM AUTHOR]