Polymerase chain reaction (PCR) assays were used to characterize 575 Escherichia coli isolates from swine submitted to the veterinary diagnostic laboratory from January through May 1998. About one-third of the isolates carried genes characteristic of enterotoxigenic (ETEC), or Shiga toxin-producing (STEC), or attaching and effacing (AEEC) E. coli pathotypes. The ETEC were the most common pathotype. The data indicate that vaccination or vaccine development based on F18 and K88 pilus antigens continues to be appropriate for the control of ETEC infections. The STEC and AEEC infections also contribute to intestinal diseases in swine but apparently at lower prevalences than ETEC in this population. Nearly 25% of the ETEC lacked genes for any of the pilus types included in the assay. It is not known if these are nonpathogenic ETEC or if they produce other (as yet undiscovered) pilus antigens. If the latter interpretation is correct, they could represent an emerging population of ETEC pathogens not reflected in current pilus-based vaccines and diagnostic tests. There were also a number of strains that carried genes for K88 or F18 pili but did not have genes for enterotoxins. It was speculated that such strains may be acting as naturally occurring live oral pilus vaccines in herds where they occur.