Tissue resident macrophages (TRMs) are multifunctional immune cells present in all tissues, contributing to the correct development, homeostasis, and protection against pathogens and injury. TRMs are morphologically and functionally heterogeneous, as a result of both the diversity of tissue environments in which they reside and their complex origin. Furthermore, some specific TRM populations are controlled by nuclear receptors. A widely used method for studying the role of nuclear receptors in immune cells is flow cytometry. Although flow cytometry is extensively used in tissues such as the peripheral blood, lymph nodes, peritoneal cavity, and bone marrow, there is a need for protocols for the study TRMs in solid tissues.In this chapter, we describe a comprehensive protocol for obtaining single-cell suspensions of resident macrophages from the pleural cavity, heart, lung, spleen, and kidney, and we present detailed gating strategies for the study of nuclear receptor activity in different TRM subsets within these tissues.