Harvard College 1 article published in JoVE Immunology and Infection Flow Cytometric Analysis for Identification of the Innate and Adaptive Immune Cells of Murine Lung Anthos Christofides1,2, Carol Cao1,2,3, Rinku Pal1,2, Halil I. Aksoylar1,2, Vassiliki A. Boussiotis1,2 1Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 2Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 3Harvard College In this study, we present an effective and reproducible protocol to isolate the immune populations of the murine respiratory system. We also provide a method for the identification of all innate and adaptive immune cells that reside in the lungs of healthy mice, using a 9-color-based flow cytometry panel.