Study on 884 children under age of 5 years old (627 diarrhea children, 257 healthy children) at 4 places: National Pediatric Hospital, Saint Paul Hospital, Thanh Nhan Hospital and Kim Lien primary school from March 2001 to April 2002. The results: the most prevalent pathogen was Rotavirus with the prevalence of 45% in children under 5 years old with diarrhea, E.Coli was the second commonly pathogen, was isolated by PCR technique with the rate of 24% in diarrhea children, 12% in healthy children and then Shigella with 3.2% in diarrhea children. No Salmonella and V.cholerae strains were identified PCR was used as effective method to indentify and differenciate diarrheagenic E.Coli strains