Microglia are highly ramified brain phagocytes that are finely tuned to surrounding neuronal and glial activity. Combined, microglia morphology, dynamic process movement, phagocytic, and neuroinflammatory responses aid in the detection of changed neuronal function, maintenance, and restoration of neural networks during physiology and pathophysiologic conditions. An awareness of how microglia diversity in the healthy brain relates to brain region and sex differences would inform brain physiology, further delineate risk factors of central nervous system (CNS) diseases, and clarify mechanisms of dichotomous injury outcomes between men and women. Microglia morphology, complement receptor 3 (CR3), and neuroinflammatory proteins were studied in the somatosensory cortex and hippocampus CA1 among male and female (estrus, diestrus and ovarian failure) mice (C67Bl/6J, 16 weeks) to discover relationships among microglia morphology, region, sex, and neuroinflammatory environment. The human post-menopause period was modeled in mice using 4-vinylcyclohexene diepoxide injections which induced accelerated ovarian failure. Using methods to quantify ramification, shape, and complexity, we discovered differences in microglia morphologies according to brain region and sex group. Microglia endpoints, process length, and complexity were increased in the female ovarian failure group when compared to other sex groups. Microglia were smaller and less complex in the hippocampus region versus the cortex. Microglia phagocytic receptor CR3 was assessed using immunohistochemistry methods and was increased in the female diestrus cortex when compared to male and females in estrus; no sex differences were observed in the hippocampus. Neuroinflammatory protein concentrations were screened using Multiplex Luminex methods and were detected in cortex homogenates, however, no differences among the sex groups were observed. Microglia morphology and CR3 are diverse in the adult healthy cortex according to region, sex and ovarian function, indicative of diversity in microglial constitutive form and function. Such differences may be influenced by parenchymal context such as neuronal and glial populations/activity or differences in sex hormone concentrations, systemically circulating or in situ, rather than by concentrations of neuroinflammatory proteins. Understanding sex and region specific differences in the brain’s surveillance and maintenance system will provide insight into the variability of patient risk and outcomes in CNS diseases.