This study was undertaken to determine the frequency of pathogenic Escherichia coli strains among wild-type E. coli strain isolates from the microbial flora of healthy volunteers and from natural residential water habitats of a defined geographic area. In total, 131 stool and 95 water isolates as well as 14 E.coli K12 strains were examined for DNA sequences specific for 20 different genes encoding E. coli pathogenicity factors, including adherence factors, toxins, invasins, capsules and iron uptake systems. The expression of the corresponding pathogenicity factors was also investigated. No pathogenicity factors were found to be present in the tested E. coli K12 strains. In contrast, 41.0% of the water samples and 63.4% of the stool samples contained pathogenicity factors specific for extraintestinal E. coli pathogens. While no virulence determinants specific for intestinal E. coli pathogens were found among the investigated environmental water isolates, 4.5% of the stool samples contained either only intestinal or both intestinal and extraintestinal virulence genes. Both the prevalence of the virulence genes and the expression of the corresponding pathogenicity factors were, in general, higher in stool than in water samples. These findings might indicate the prevalence of different clonal types and/or differential regulation of pathogenicity factor expression in diverse ecological niches.