Background: Acute gastroenteritis (AGE) remains a global public health problem. Rotavirus (RV), norovirus (NoV) and Sapovirus (SV) are recognized as an important causes of AGE among children worldwide. However, there is no information about prevalence of Sapovirus infection in Iraq. Objective: To assess the frequency of SV, RV and NoV in children with AGE, also to determine the risk factors associated with the disease. Methods: A cross section study was carried out for 93 children under the age of five years old with AGE who attended to the Emergency Department of Pediatrics in Al-Batool Teaching Hospital for Maternity and Children in Baqubah city, Iraq, using real-time Polymerase Chain Reaction (RT-PCR) to determine the presence of human Sapovirus nucleic acid and enzyme-linked immunosorbent assay (ELISA) to evaluate the presence of human rotavirus and human norovirus antigens. Results: The positive samples of SV were (6.5%). And the positive samples of RV and NoV were (79.6%) and (1.1%), respectively. Statistically, RV shows the higher positivity rate among viruses with significant difference (P<0.05). The present study showed that all SV and NoV cases were coinfected with RV. In addition, the present study showed that there was no statistically significant association between viruses positivity and the different sources of water, the level of mother education and clinical features (P>0.05). Conclusion: RV can be consider one of the most causes of diarrhea in children and more research are required to investigate the role of SV as a primary etiology of pediatric diarrhea.