Defensins are important antimicrobial effector peptides of the innate immune system, which provides protection against bacterial infections in the intestine. Salmonella Choleraesuis and Salmonella Typhimurium are the most commonly isolated serovars in pig, but disease outcome is dependent on the Salmonella serovar. These infections are a serious problem for the swine industry and are also posing a major threat to public health because of Salmonella-related food-borne illnesses in human. To understand the innate immune response of pigs upon Salmonella infections, we studied the effect of these Salmonella serovars on defensin gene expression in the porcine ileal epithelial cell line IPEC-J2. With the use of scanning electron microscopy, we first visualized the surface characteristics of this cell line, and captured the invasion of Salmonella into the epithelial cell. Gene expression levels of porcine beta-defensin 1 and 2 were both induced upon S. Typhimurium infection but S. Choleraesuis had no effect. Invasion, adhesion and defensin susceptibility of both serovars were similar, which could not explain the observed difference in host response to these Salmonellae. In addition, induction of defensins was dependent on viability of S. Typhimurium, since Salmonella cell- or secreted components had no effect on defensin gene expression. These results provide further insight into the porcine innate immune response towards Salmonella infections, and could partially explain the different epidemiology of Salmonella infections in pig.