Streptococcus (S.) suis and Mycobacterium avium ssp. paratuberculosis (MAP) differ substantially in their host specificity and tissue tropism. S. suis is a facultative pathogen in swine, which mainly colonises the upper respiratory tract and can cause meningitis, septicemia, arthritis and pneumonia. In contrast, MAP is an obligatory pathogen causing paratuberculosis in ruminants, and shows high tropism for the intestinal tract. Both pathogens are able to invade and persist in host cells. In S. suis, the significance of invasion for pathogenesis is a matter of controversial discussions. In vitro it has been shown that S. suis is internalized by epithelial cells and survives intracellularly for at least 24 h. However, at present there is no evidence that S. suis invades epithelial cells also in vivo. In MAP, on the other hand, persistence in macrophages is generally considered a crucial step in pathogenesis, but it remains to be elucidated, how it contributes to pathophysiology of the disease. The two pathogens exemplify how intracellular invasion and persistence might play different roles in pathogenesis. In S. suis, intracellular life may represent only a transient retreat phase, whereas in MAP it is the predominant in vivo niche of the pathogen.