Microglia play key immunological roles in the central nervous system. Upon activation, resident microglial cells transform from a ramified form to an amoeboid form and acquire the ability to phagocytose and release pro-inflammatory cytokines. Here, we review microglial phenotypes that contribute to their functional roles in the central nervous system with the emphasis on their molecular profiles. Deeper understanding of the functions performed by microglia in physiological and pathological conditions can promote investigation of microglia activities in brain injury or disease and facilitate development of new treatment approaches.