Macrophages are part of the innate immune system, recognizing, engulfing, and destroying many potential pathogens including bacteria, pathogenic protozoa, fungi, and helminths. The destructive potential of macrophages and their ability to secrete regulators of the function of neighboring cells contribute to many aspects of homeostasis. This chapter talks about the origins, differentiation, and functions of macrophages throughout the body. The study of mononuclear phagocyte biology in vivo was expedited by the advent of monoclonal antibodies that recognize some of the macrophage restricted molecules, as well as surface proteins of an unknown function. Embryonic phagocytes appear in the yolk sac and embryo proper before the formation of blood circulations and the occurrence of hepatic hematopoiesis. The regulation of functions of the macrophages requires expression of macrophage specific genes, which, in turn, is likely to involve a number of lineage-specific transcription factors. Peritoneal macrophages are the most studied primary macrophages in mice because they are easily isolated by peritoneal lavage. The splenic macrophages are an important component of the innate immune system, as evidenced by the incidence of septicemia following splenectomy. Microglia are the resident macrophage population in the normal healthy adult nervous system. Ovarian macrophages are mainly found in the interstitium, being excluded from the germ cell compartment, except in atretic follicles where macrophages are recruited for the destruction of defunct follicle. The availability of macrophage-specific transgenes, and transgenic approaches to lineage tracing, will provide new opportunities to explore the true function of this family of cells.