The genus Aeromonas comprises known virulent and avirulent isolates and has been implicated in waterborne disease. A common infection model of human gastroenteritis associated with A. hydrophila uses neonatal mice. The goal of this research was to evaluate whether a murine small intestinal cell line could provide comparable results to the gene expression changes in the neonatal mouse model. Changes in mRNA expression in host cell cultures and intestinal tissues were measured after exposure to virulent Aeromonas hydrophila strains. A. hydrophila caused the up-regulation of more than 200 genes in neonates and over 50 genes in cell culture. Twenty-six genes were found to be in common between the two models, of which the majority are associated with the innate immune response.