Intussusception is a common pediatric emergency in Egypt. The high morbidity and mortality from Rotavirus-associated diarrhea led to development an oral vaccine against the virus. During post-licensure surveillance, a strong association was noted between the vaccine and intussusception resulting in vaccine withdrawal. Aim of the work is to determine the risk factors underlying the development of intussusception among an Egyptian pediatric population and to ascertain in particular whether an association between native Rotavirus infection and the development of intussusception in Egypt.In this prospective study, 73 cases with the diagnoses of intussusception and 214 controls were involved. Stool samples, throat swabs and blood samples were collected and analyzed for Rotavirus.