Microglia are innate immune cells that survey the central nervous system (CNS) and respond almost immediately to any disturbance in CNS homeostasis. They are derived from primitive yolk sac myeloid progenitors and in the mouse colonize the CNS during fetal development. As a population, microglia have the potential to expand rapidly in response to inflammatory stimuli, injury, or any other pathological changes, due to a high capacity for proliferation. In addition, apoptotic mechanisms can be evoked to retract the microglial population, as reactivity declines. In the normal CNS, a low rate of proliferation and apoptosis maintain a low rate of microglial turnover. Here, we describe quantitative analysis of proliferation and apoptosis of microglial cells isolated from individual adult mice by flow cytometry, which allows distinction from perivascular or infiltrating macrophages, based on differential expression of CD45. These methods can be applied to analyze microglial turnover in various models of neuroinflammation.