Food poisoning and diarrhea is one of the common health problems in the world. Diarrhea can be caused by many organisms but E. coli has been recognized to be the frequently caused main pathogen. Among them most important are EPEC and non-O157. EPEC causes the severe diarrhea in infants and sometime in adults. It has been the cause of diarrhea since more than 40 years. Non-O157 E. coli is the emerging diarrheagenic pathogen. It also causes HUS in human which remains the major health problem. But no detailed research and characterization have been made yet. Recently, more attentions have been focused on infections caused by non-O157 E. coli isolates. Both EPEC and non-O157 E. coli produce Verotoxin (VT) gene. No detailed molecular characterization of EPEC and non-O157 E. coli isolates in relation with VT gene was carried out in Malaysia. In this study, EPEC and non-O157 E. coli isolates were collected and molecular characterizations were carried out in relation to VT gene. The new findings presented here will provide a significant improved knowledge for better understanding for this highly significant emerging non-O157 E. coli pathogen in relation to its verotoxin production.