During the last 10 years, different subsets of Innate lymphoid cells (ILCs) have been identified in murine models. ILCs play and important role in maintaining immune barriers, tissue homeostasis, and are able to regulate the immune response in several anatomic sites. They can be found in lymphoid and non-lymphoid organs of adult mice but are mainly tissue-resident cells that can expand locally under physiologic or pathologic conditions (Gasteiger, Fan, Dikiy, Lee, & Rudensky, 2015). Because ILCs need to be identified by a complex combination of several cell-surface and intracellular markers and by their production of specific sets of cytokines, multiparametric flow cytometry remains one of the most efficient methods to analyze and isolate the different ILC sub-populations. This chapter describes how ILCs can be identified in different murine organs and how ILC subsets can be isolated and functionally analyzed.