Abstract: Microglia have multiple functions and phenotypes that can prevent or worsen neuropathology.  Microglial depletion and repopulation methods provide a promising technique for understanding microglial biology. Their utility as therapeutic modalities is now under consideration. As resident immune cells in the central nervous system (CNS), microglia maintain the local environment and promote neuronal vitality. However, persistent proinflammatory signaling due to aberrant microglial activation can be detrimental. This is seen in settings such as traumatic brain injury (TBI) (Henry et al., 2020), stroke (Li et al., 2017), and alcohol use disorder (AUD) (Coleman et al., 2020), when the loss of homeostatic control results in persistent proinflammatory signaling that contributes to ongoing neuropathology (Figure 1). Thus, selective replacement of chronically proinflammatory-activated microglia could improve functional outcomes. Depletion of microglia from the CNS microenvironment has served as a helpful tool to understand the contribution of microglia to brain disease. In this perspective, we discuss our recent findings regarding microglial depletion and repopulation in AUD as well as the benefits and detriments of microglial depletion and repopulation and their potential therapeutic applications in other neuropathological disease models. We recently reported that microglial depletion and repopulation protected against long-term proinflammatory activation in a model of AUD (Coleman et al., 2020). In a primary ex vivo brain slice culture model, binge ethanol caused a persistent induction of proinflammatory cytokines. Microglial depletion and repopulation after ethanol treatment, using methods described below, resulted in a normalization of proinflammatory cytokines to baseline levels, and an increase in protective trophic factors such as brain-derived neurotrophic factor. Thus, repopulation of microglia could potentially reverse neuropathology associated with chronic proinflammatory signaling in AUD and other proinflammatory neurological diseases (Figure 1).