Introduction: Acute diarrheal diseases remain the leading cause of morbidity among infants and young children in Egypt. Determination of the frequency of diarrhea in an area, along with the proportion of disease caused by specific enteric agents of different origin, is considered the first step in controlling diarrheal diseases. Methodology: During the period from July 2009 to June 2010, 206 stool samples were collected from children younger than 5 years suffering from diarrhea in the gastroenteritis outpatient clinic of Abu El Reesh El Mounira Pediatric Hospital, Cairo University. Stool samples were examined for enteric pathogens using a combination of culture, enzyme immunoassay (EIA) and polymerase chain reaction (PCR) methods. Results: Pathogens were detected in 180 (73.4%) of stool samples. Mixed infections were detected in 119 (57.8%) of stool samples. The prevalence of enteropathogens identified was as follows: EAEC (48%), rotavirus (33.2%), ETEC (24.7%), EPEC/ E. albertii (18%), Campylobacter spp (14.1%), G. lamblia (13.5%), Cryptosporidium spp (12.5%), Shigella/ EIEC (11.7%), norovirus (5.5%), astrovirus (4%). Salmonella spp (1.5%), P. shigelloides (1%), adenovirus (1%) and Aeromonas hydrophila (0.5%). Antibiotic resistant bacterial strains were high in our study. Conclusion: In our study, the incorporation of cultural, immunoassay and molecular techniques yielded useful data in identifying pathogens in previously pathogen-negative diarrhea cases.