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Purpose Paneth cells are important regulators of host-microbe interactions at mucosal surfaces, playing a key role in innate immunity by secreting antimicrobial peptides into the small intestinal lumen. Some pathogenic bacteria have developed virulence mechanisms that have allowed them to inhibit expression and/or function of these antimicrobial peptides. Helicobacter hepaticus , a mammalian pathogen, localizes to the cecum and intestinal crypts. H. hepaticus possesses a cytolethal distending toxin (CDT), which modulates the host immune system and is essential for long-term intestinal colonization. Therefore, we set about determining whether H. hepaticus might down-regulate the expression of Paneth cell antimicrobials as one of its virulence mechanisms during infection, thereby facilitating H. hepaticus colonization. Methods Samples of distal small intestine obtained 2 weeks after bacterial inoculation were analyzed from three groups of mice: uninfected wild-type C57BL/6 mice, mice infected with H. hepaticus , and mice infected with an isogenic H. hepaticus CDT mutant. Quantitative real-time PCR was performed using external standards to determine the absolute values of mRNA levels of 21 target genes, which included mouse Paneth cell antimicrobial peptides, other Paneth cell products, cytokines, and other intestinal antimicrobials. The data were analyzed using Student9s t -test. Results In mice infected with H. hepaticus , the cytokines KC (a human interleukin-8 equivalent) and tumor necrosis factor α (TNF-α) showed significant increases in expression when compared with levels in uninfected mice, consistent with mucosal inflammation in the infected samples. Other genes showed no changes in expression levels when comparing uninfected wild-type mice to mice infected with H. hepaticus . Little or no effect was seen on the expression of any tested genes with infection of the isogenic H. hepaticus CDT mutant. Conclusion Our data do not support the hypothesis that H. hepaticus infection down-regulates expression of Paneth cell products. There is evidence that H. hepaticus infection stimulates changes in the host defense response, specifically, increasing expression of the cytokines KC and TNF-α. The mechanism(s) by which H. hepaticus evades the innate immune defense mechanisms of Paneth cells remains a topic for further study.