In epidemiological studies of infectious disease, researchers often rely on specific cues of the host, such as clinical signs, as surrogate indicators of pathogen presence. A selection bias would manifest if the specific visual cues used in sampling for the pathogen were not representative of the full range of signs caused by the strains of that pathogen. In our molecular epidemiological studies of Escherichia coli associated with avian cellulitis in broilers, we collect carcasses at the processing plant based on visual cues of lesion morphology. Therefore, the objectives of this study were to: (1) explore the potential impacts of selection bias in an application of infectious disease epidemiology, and (2) utilize a validation protocol to assess the potential for selection bias in our molecular epidemiological studies of E. coli and avian cellulitis. In two different trials, E. coli DNA fingerprints were compared between birds that our observers collected and the birds that the observers missed. Using Fisher's exact tests and simulation models, we determined that the isolates collected by the observers were not significantly different from the isolates missed by the observers (P > 0.60 in both trials). Our method of selecting birds suspected of having cellulitis did not significantly bias our inferences about the population of E. coli associated with cellulitis in the flock. We encourage more investigators to critically assess the relationship of the sample to the target population in epidemiological studies of infectious disease.