Background: Sporozoan protozoa and enteroparasites cause gastroenteritis. Sporozoa are the major cause of self-limiting diarrhea in immunocompetent patients, however they cause serious diseased in patients with immunosuppression. Objectives: The current study aimed to identify the prevalence of sporozoa and enteroparasites among patients with gastroenteritis referred to the healthcare centers in seven provinces of Iran. Patients and Methods: In this cross-sectional study, 4200 stool samples were randomly collected from patients with gastroenteritis in the selected hospitals of Gilan, East Azerbaijan, Qazvin, Kurdistan, Mazandaran, Tehran and Khorasan-e-Razavi provinces. Primarily samples were examined directly for enteroparasites. The samples were then filtered and concentrated using Paraseb kit. The pellets were fixed, stained by different assays including acid fast staining, Auramin Phenol Fluorescence, Giemsa and light microscopy. Results: The results revealed the overall rate of infection, 3.86% (163 cases), as an indicator of parasitic enteropathogens in Iran. Among the provinces, Khorasan-e-Razavi and Mazandaran with 8.83% (53 cases) and 0.34% (2 cases) showed the highest and lowest rates of infection, respectively. The frequencies of sporozoa including Cryptosporidium, Microsporidium, Isospora and Cyclospora spp. were 0.1%, 0.1%, 0.07% and 0.02% respectively. Among the parasites, Giardia lambelia, Taenia saginata and Hookworms with 1.78% and 0.02% had the highest and lowest rates of infection, respectively. Regarding the age groups, the highest and the lowest rates of infection were in 0 - 10 (48%) and 41 years old and above (6.7%) groups, respectively. Conclusions: Despite relatively low prevalence of sporozoa, giardiosis is the most prevalent agent for gastroenteritis amongst 3.86% of parasitic infections in Iran. The current study confirmed the abundance of infection in warm and wet seasons, and more frequency of infections among children than adults. Meanwhile, geographical and agricultural conditions, seasonal rainfall, abundance of water, and animal contact are key factors affecting sporozoan infections.