The prevalence and characteristics of eae- and stx-positive Escherichia coli strains in wild birds in the immediate environment of Tokyo Bay, Japan, was examined using cloacal swab samples taken from 447 birds belonging to 62 species. PCR screening showed that the prevalences of stx- and eae-positive strains of Escherichia coli were 5% (23/447) and 25% (113/447), respectively. Four strains of stx(2f)-positive E. coli were isolated from two feral pigeons, an oriental turtle dove and a barn swallow. In contrast, 39 eae-positive E. coli strains were isolated, and most of the strains possessed a subtype of intimin that is classified as a minor group of human intimins, such as intimin upsilon, kappa, and mu. Moreover, these strains did not possess any of the other pathogenic genes tested, such as stxs, ehxA, bfp, or irp. Thus, wild birds were considered to be a reservoir of atypical enteropathogenic E. coli.