In the present study, we examined the prevalence and characteristics of CTEC among diarrheal children in Japan during a year-long surveillance study. A PCR-RFLP assay for the detection and differentiation of five types of E. coli cdtB gene (types I through V) was developed, and 362 stool specimens collected from patients reporting to pediatric departments in two hospitals were analyzed. Of the 35 samples (9.7%) that were positive for the cdtB gene, 21 were positive for cdt-I, three for cdt-II, four for cdt-III, three for cdt-IV and four samples were positive for cdt-V, as determined by different molecular techniques. The recovery of CTEC having cdt alleles was a little less, which included 19 with cdt-I, one cdt-II, three cdt-III, three cdt-IV and four with cdt-V. Among 30 CTEC strains isolated, the majority of them (43%) belonged to serogroup 02. The other virulence genes such as astA, cnfl, eaeA, cnf2 and bfpA genes were detected in 14 (47%), 11 (37%), four (13%), three (10%) and one (3.3%) strains of CTEC, respectively. However, the other common virulence-associated genes specific for DEC were not detected in these strains. Interestingly, an untypable cdt gene was detected by PCR-RFLP in Providencia alcalifaciens. Our data indicate that CTEC may be associated with diarrheal children in Japan and most of them do not belong to a conventional enteropathogenic pathovar and thus differ from strains isolated in developing countries.