Background: Acute infectious gastroenteritis is a common cause of fatality between children in the developing countries which is usually due to viral etiology. Rotavirus is a ds-RNA (60-80nm), non-enveloped virus with a segmented genome. Group (A) of the virus is an important human pathogen that accounts for (90%) of the isolates. An easy, rapid, non-expensive and sensitive method is needed to detect this virus for clinical controlling. The objective of this study is to evaluate Enzyme immunoassay technique versus Quantitative real-time PCR in the diagnosis of infection with Rotavirus in the children with acute diarrhea. Methodology: This study was conducted on (75) infants and young children, from The Pediatric Department at Tanta University Hospitals in the period from December 2019 to March 2020 and were diagnosed according to history and clinical examination using Vesikari scoring system for acute severe gastroenteritis. Also, 10 healthy infants and children were taken as a control group. Stool samples were obtained from the patients and the controls. These specimens were tested with ELISA and Quantitative real-time PCR for detection of Rotavirus in stool. Results: The study revealed that 62 patients (82.6 %) were positive by ELISA and 74 cases (98.6 %) were positive with real time RT-PCR. Additionally, all the control group gave negative results by the two techniques. Conclusion: Enzyme immunoassay is an accurate and suitable method as a routine diagnostic measure for Rotavirus that can run a large number of samples. But, it is expensive when used for a single sample. Quantitative real time PCR was more sensitive and specific measure that can detect Rotavirus RNA in too minimal amounts in stools.