The mononuclear phagocyte system (MPS) is composed of monocytes, macrophages and dendritic cells (DCs) and has crucial roles in maintaining organismal homeostasis. In addition, the diverse activities of the MPS are relevant in inflammation, autoimmunity, infection, cancer and organ transplantation. Commitment to the mononuclear phagocyte lineage is determined at the stage of the mac- rophage and DC progenitor (MDP), at which point, eryth- roid, megakaryocyte, lymphoid and granulocyte fates have been precluded (FIG. 1). MDPs give rise to monocytes and common DC progenitors (CDPs) 1,2 . Whereas monocytes can directly participate in effector immune responses or differentiate into macrophages or DCs, the differentiation potential of CDPs is restricted to the DC lineage (FIG. 1). CDPs give rise to plasmacytoid DCs and pre-DCs, which subsequently give rise to DCs 3–5 . Plasmacytoid DCs have been recently reviewed and will not be further covered in this manuscript 6 . How cell fate is decided, including the factors that drive MDP differentiation and the genes responsible, is still not well known. What is becoming increasingly clear is that monocytes, macrophages and DCs are not homogenous populations. Just as CD4 + T cells further differentiate into distinct subsets (such as T helper 1 (T H 1), T H 2, T H 17 and regu- latory T (T Reg ) cells), monocytes, macrophages and DCs can also differentiate into discrete functional subsets. The monocyte population is composed of two main subsets in mice and humans, designated classical monocytes and non-classical monocytes, and these cells are found primarily in the circulation, bone marrow and spleen 7 . Macrophages are found in all tissues throughout the body from embry- onic to adult life. Macrophages are well known for their functions in protecting the host from pathogens and their roles in clearing dead cells, but they also have unique func- tions that are influenced by their locations in the body. For example, bone marrow macrophages promote stromal retention of haematopoietic stem and progenitor cells 8 , and lymph node subcapsular sinus macrophages prevent central nervous system (CNS) invasion after peripheral infection with a neurotropic virus 9 . DCs were originally distinguished from macrophages by their increased ability to activate T cells in an antigen- dependent manner, and these cells are also found in lymphoid and non-lymphoid tissues. Whereas macro- phage heterogeneity is classified based on tissue location, the two main DC subsets are characterized by differential requirements for transcription factors and distinct origins. The transcription factors inhibitor of DNA binding 2 (ID2), interferon-regulatory factor 8 (IRF8) and basic leucine zipper transcriptional factor ATF-like 3 (BATF3) are the basis for this distinction. Although lymphoid tissue CD8 + DCs and non-lymphoid tissue CD103 + DCs (collec- tively termed BATF3-dependent DCs) require ID2, IRF8 and BATF3 for their development, lymphoid tissue CD8 – DCs and non-lymphoid tissue CD11b + DCs (collectively termed BATF3-independent DCs) develop independently of these factors 10–14 . The BATF3-dependent DC subset is completely derived from a circulating pre-DC, but at least some BATF3-independent DCs arise from circulating monocytes 11,12 (FIG. 1). There are a number of outstanding questions about the development, homeostasis and function of MPS cells. Although several subsets of monocytes, macrophages and DCs have been identified, the individual contribu- tions of these subsets to health and disease are not well known, and it is probable that additional, functionally distinct subsets exist. Moreover, few of the relevant genes involved in the development and function of MPS cells have been characterized. Over the last few decades, a number of tools have been developed to address these *Departments of Oncological Sciences and Medicine, Mount Sinai School of Medicine, New York, New York 10029, USA. ‡ Immunology Institute, Mount Sinai School of Medicine, New York, New York 10029, USA. § Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA. ¶ Tisch Cancer Institute, Mount Sinai School of Medicine, New York, New York 10029, USA. Correspondence to M.M. e-mail: miriam.merad@mssm.edu doi:10.1038/nri3087 Monocytes Monocytes are mononuclear phagocytes that circulate in the blood. Monocytes are thought to differentiate into macrophages and some dendritic cells in peripheral tissues. They consist of two subsets: classical monocytes and non-classical monocytes. Studying the mononuclear phagocyte system in the molecular age Andrew Chow*, Brian D. Brown ‡§ and Miriam Merad* ‡¶ Abstract | The mononuclear phagocyte system (MPS) comprises monocytes, macrophages and dendritic cells. Tissue phagocytes share several cell surface markers, phagocytic capability and myeloid classification; however, the factors that regulate the differentiation, homeostasis and function of macrophages and dendritic cells remain largely unknown. The purpose of this manuscript is to review the tools that are currently available and those that are under development to study the origin and function of mononuclear phagocytes. REVIEWS 788 | NOVEMBER 2011 | VOLUME 11 www.nature.com/reviews/immunol REVIEWS © 2011 Macmillan Publishers Limited. All rights reserved