The objective of the study was to describe the etiology, epidemiology, and clinical characteristics of the principal causes of acute infectious diarrhea requiring hospitalization among children under 5 years of age in Rabat, Morocco. A prospective study was conducted from March 2011 to March 2012, designed to describe the main pathogens causing diarrhea in hospitalized children >2 months and less than 5 years of age. Among the 122 children included in the study, Enteroaggregative E. coli (EAEC) and rotavirus were the main etiologic causes of diarrhea detected. Twelve (9.8%) children were referred to the intensive care unit, while 2, presenting infection by EAEC and EAEC plus a Shigella sonnei respectively, developed a hemolytic uremic syndrome. Additionally, 6 (4.9%) deaths occurred with EAEC being isolated in four of these cases. Diarrheogenic E. coli and rotavirus play a significant role as the two main causes of severe diarrhea while other pathogens such as norovirus or parasites seem to have a minimal contribution. Surveillance and prevention programs to facilitate early recognition and improved management of potentially life-threatening diarrhea-episodes are needed.