Purpose: Diarrheal diseases are a major cause of morbidity and mortality among children in developing countries. Among the bacterial pathogens, diarrheagenic E. coli (DEC) are the most common agents causing diarrhea worldwide. The objective of this study was to determine the prevalence of DEC in stool samples from children with acute diarrhea using polymerase chain reaction (PCR). Methods: A total of 75 stool samples from children under the age of 15 with acute diarrhea were collected by aseptic measures for a period of one year. The selected samples were screened for E.coli by standard microbiological methods. Identification of pathogenic E.coli was based on cultural characters and standard biochemical reactions. The E.coli isolates were subjected for PCR analysis to classify as EPEC, EAEC, STEC and ETEC strains using their virulence marker genes. Results: 17 (23%) DEC isolates were identified from 75 stool samples. EPEC showed high prevalence (12%) followed by EAEC (5.33%) and STEC (4%). No ETEC strains were isolated from the population. Conclusion: The study showed that EPEC (12%) is the predominant strain among other DEC in causing diarrhea among children.