Salmonella is among the top-ranked foodborne pathogen, inducing a wide variety of diseases ranging from gastroenteritis to typhoid fever. It is a facultative intracellular pathogen that enters phagocytic and non-phagocytic cells. After host cell invasion, intracellular survival is permitted by Salmonella entry into an endocytosis vesicle called the “Salmonella-containing vacuole” (SCV) where Salmonella moderately replicates. However, it has recently been shown that Salmonella uses the PagN protein to escape from the SCV to establish an intra-cytosolic replicative niche in the host cell. Currently, the cells in which Salmonella escapes from the vacuole and its dependence or not on PagN, in vivo, remain unknown. In this study, we developed two methods to identify, in vivo, the Salmonella-infected epithelial and immune cells, the subcellular localization of bacteria and PagN transcription in the cecum in a murine model of gastroenteritis. Our work suggested that Salmonella Typhimurium infects many cell types. Moreover, within caecal epithelial cells, it can also escape from the SCV to establish an intra-cytosolic niche leading to hyper-replication, responsible for its massive dissemination in vivo. Also, pagN transcription was detected within several cell types. This work allowed a better understanding of the interactions of Salmonella with host cells and could be extended to typhoid and carrier state models in order to better characterize the interaction of Salmonella with host cells according to the disease induced.