Typhoid fever and salmonellosis, which are caused by Salmonella Typhi and Typhimurium respectively, are responsible for significant morbidity and mortality in both developed and developing countries. We model typhoid fever using mice infected with Salmonella Typhimurium, which results in a systemic disease, whereby the outcome of infection is variable in different inbred strains of mice. This model recapitulates several clinical aspects of the human disease and allows the study of the host response to Salmonella Typhimurium infection in vivo. Previous work in our laboratory has identified three loci (Ity, Ity2 and Ity3) in the wild-derived MOLF/Ei mice influencing survival after infection with Salmonella Typhimurium. Fine mapping of the Ity3 locus indicated that two sub-loci contribute collectively to the susceptibility of B6.MOLF-Ity/Ity3 congenic mice to Salmonella infection. In the current paper, we provided further evidence supporting a role for Ncf2 (neutrophil cytosolic factor 2 a subunit of NADPH oxidase) as the gene underlying the Ity3.1 sublocus. Gene expression profiling indicated that the Ity3.1 sub-locus defined a global gene expression signature with networks articulated around Ncf2. Furthermore, based on differential expression and complementation analysis using Selp (Selectin-P) knock-out mice, Selp was identified as a strong candidate gene for the Ity3.2 sub-locus.