The bone marrow (BM) is an important site for the interrelated processes of hematopoiesis, granulopoiesis, erythropoiesis, and lymphopoiesis. A wide variety of microbial challenges are associated with profound changes in this compartment that impact on hematopoietic differentiation and mobilization of a variety of cell types. This article reviews some of the key pathways that control BM homeostasis, the infectious and inflammatory processes that affect the BM, and how addressing the knowledge gaps in this area has the potential to widen our comprehension of immune homeostasis.