The clinical documentation of enteropathogenic bacteria causing diarrhea in dogs is clouded by the presence of many of these organisms existing as normal constituents of the indigenous intestinal flora. The diagnosis of a putative bacterial enteropathogen(s) in dogs should be made based on a combination of parameters, including signalment and predisposing factors, clinical signs, serologic assays for toxins, fecal culture, and PCR. Relying on results of fecal culture alone is problematic, because C perfringens, C difficile, Campylobacter spp, and pathogenic and non-pathogenic E coli are commonly isolated from apparently healthy dogs [10,13,33]. Nevertheless, culture may be useful in procuring isolates for the application of molecular techniques, such as PCR, for detection of specific toxin genes or molecular typing of isolated strains to establish clonality in suspected outbreaks. The oversimplistic attempt to characterize bacterially associated diarrhea by anatomic localization of clinical signs should be discouraged, because most of the previously mentioned bacteria have been associated with small and large intestinal diarrhea. Accurate diagnosis of infections may require diagnostic laboratories to incorporate PCR-based assays using genus- and species-specific primers to facilitate detection of toxin genes and differentiation of species that appear phenotypically and biochemically similar. There has been tremendous interest in the application of microarray technology for the simultaneous detection of thousands of genes or target DNA sequences on one glass slide. This powerful tool could be used for detection of specific pathogenic bacterial strains in fecal specimens obtained from dogs in the future.