Macrophages serve as an effective component of innate immunity in their ability to recognize, engulf and kill potential pathogens. They also coordinate additional host responses by synthesizing a range of inflammatory mediators that can activate the adaptive immune response and establish protective immunity. Although they are a key component of mammalian defense system, macrophage activity is not always beneficial to the host. The centrality of macrophages in disease processes makes macrophage regulation a major target in the prevention, control and cure of inflammatory processes. Consequently, macrophage-restricted genes may be crucial targets for therapeutic intervention. A review is presented of the use of large-scale cDNA microarrays to compare macrophage inflammatory genes differentially expressed in two distinct macrophages populations--bone marrow derived macrophages (bmm) and inflammatory thioglycolate-elicited peritoneal macrophages (tepm)--to non-macrophage cell populations consisting of primary embryonic fibroblast and spleen non-adherent cells. Expression profiles indicate that macrophage inflammatory genes are associated with expected functional categories, such as lysosomal degradation, phagocytosis, host defense and homeostasis.