Salmonella typhimurium infection in mice is focused on the spleen and liver, and prolonged infection can lead to sepsis and death. After intravenous infection with a moderate dose of S. typhimurium, the few bacteria that survive in the spleen and liver grow in a 'safe-site' where they are protected from immune destruction. In this study, we demonstrated that the lack of killing of resident salmonella in the spleen and liver was not because the salmonella were transformed within the host and became resistant to killing, or because the infected mice lost the ability to kill salmonella. We showed that the salmonella were within an intracellular 'safe-site' that protected them from killing. Brief treatment of salmonella-infected mice with gentamicin reduced the numbers of salmonella in the blood but had no effect on the numbers in the liver and spleen, suggesting an intracellular location of the salmonella. After dissociation of spleen cells from recently infected mice, 60% of the salmonella remained cell associated. These cell-associated salmonella, unlike cell-free salmonella, were resistant to killing by gentamicin. The cell-associated salmonella were rendered susceptible to gentamicin after sonication, providing confirmation of their previous intracellular location.