Calorie restriction (CR) has been shown to increase longevity and elicit many health promoting benefits including delaying immunosenescence and attenuating neurodegeneration in animal models of Alzheimer's disease and Parkinson's disease. CR also suppresses microglial activation following cortical injury and aging. We previously demonstrated that CR attenuates lipopolysaccharide (LPS)-induced fever and shifts hypothalamic signaling pathways to an anti-inflammatory bias; however, the effects of CR on LPS-induced microglial activation remain largely unexplored. The current study investigated regional changes in LPS-induced microglial activation in mice exposed to 50% CR for 28days. Immunohistochemistry was conducted to examine changes in ionized calcium-binding adapter molecule-1 (Iba1), a protein constitutively expressed by microglia, in a total of 27 brain regions involved in immunity, stress, and/or thermoregulation. Exposure to CR attenuated LPS-induced fever, and LPS-induced microglial activation in a subset of regions: the arcuate nucleus (ARC) and ventromedial nucleus of the hypothalamus (VMH) and the subfornical organ (SFO). Microglial activation in the ARC and VMH was positively correlated with body temperature. These data suggest that CR exerts effects on regionally specific populations of microglia; particularly, in appetite-sensing regions of the hypothalamus, and/or regions lacking a complete blood brain barrier, possibly through altered pro- and anti-inflammatory signaling in these regions.