We examined mRNA expression of 11 genes: BAK, Bcl-x, Interferon [IFN]-gamma, Interleukin [IL]-1beta, IL-6, IL-10, IL-12alpha, IL-12beta, IL-18, CXCLi2 [IL-8/CAF], and a MIP family chemokine, CCLi2, in the spleen and cecum of day-old chicks after oral inoculation with Salmonella enteritidis (SE) or medium. Three distinct chicken breeds (broiler, Fayoumi, and Leghorn) were evaluated for mRNA expression levels at 2 and 18h post-inoculation using quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). SE exposure significantly increased splenic IL-18 and IFN-gamma expression. Breed effect was significant (P<0.05) for CXCLi2, IL-10, IL-12alpha, and CCLi2 mRNA expression in the spleen, and for IL-12alpha, IL-12beta, IL-18, and CCLi2 mRNA expression in the cecum. Generally, mRNA expression levels were higher in the spleen, and lower in the cecum, of Leghorns versus broilers. These results support a role for breed genetics influencing cytokine mRNA expression in young chickens and may potentially explain some generalized immune response differences between breeds.