Many infectious diseases are associated with parasite persistence, often restricted to certain tissue sites, yet the determinants of such persistence are poorly understood. Infection with the protozoan parasite Leishmania donovani has proved a useful experimental tool to address how immune responses can be differentially effective in clearing parasites from different tissues and, conversely, it might also provide a good model for understanding the basis of parasite persistence. This article reviews recent studies on the determinants and consequences of persistent parasite infection in the spleen and suggest that some of the messages to emerge could have important implications for the study of a broad range of infectious diseases.