Macrophages in lymphoid organs exhibit a wide variety of phenotypes and functions. These cells excel in the removal of apoptotic cells that arise during the generation of immune cells and are thereby essential for the prevention of auto-immune responses. In addition to this macrophages in the secondary lymphoid organs form an important barrier for spreading of infections by phagocytosis of pathogens and the activation of both innate and adaptive immune responses. Thus, the remarkable ability of macrophages to phagocytose and handle a wide range of self and non-self material and to produce immunomediators is effectively exploited within lymphoid organs to regulate immune activation.