Salmonella is an important foodborne pathogen and represents a common cause of gastroenteritis world-wide. Layer hens are a potential source of Salmonella that can result in egg contamination. While Australian layer industry generally maintains high safety and quality standards, eggs and egg-products are frequently implicated in Salmonella disease outbreaks. Salmonella Typhimurium is one of the most common causes of salmonellosis outbreaks but there are other non-typhoidal Salmonella serovars commonly isolated from layer farms. Little is known, however, about their pathobiology in relation to S. Typhimurium. Twenty-nine Salmonella serovars commonly isolated from egg farms were selected for this study. The comparative pathogenicity of these serovars was characterised using the human intestinal epithelial cell (Caco-2) invasion assay and virulence typing by PCR. Data obtained from cell invasion experiments showed that there were three distinct invasion patterns low, moderate, and high. PCR virulence typing was performed using 30 selected genes involved in intestinal invasion, survival, as well as flagellar and fimbrial genes. There was however, no correlation between the presence or absence of a PCR product and in vitro invasiveness. Consequently, a subset of ten total Salmonella serovars was selected from low, moderate and high invasive groups for whole genome sequencing with the aim of identifying genomic differences contributing to variation in pathogenesis. Analyses were primarily focussed on virulence genes located within the Salmonella pathogenicity island 1 (SPI-1), SPI-2, SPI-3, SPI-4, and SPI-5. Insertions, deletions, and amino acid substitutions in several virulence genes that could potentially contribute to variable pathogenicity amongst Salmonella serovars have been identified. In addition, results obtained from in vivo mouse experiments using BALB/c mice illustrated that the invasive S. Typhimurium phage types were the most pathogenic. Interestingly, S. Virchow, which had high invasion capacity in in vitro invasion experiments, exhibited low virulence in BALB/c mice.