Microglial morphology is difficult to quantify. Currently, there are no agreed upon systemic method of quantification of microglial morphology within the healthy brain or in response to an injury. Studies have proposed myriad models of morphological changes in microglial reactivation and recent studies have found sex differences in microglia. To examine changes in the microglia of murine hippocampus, we immunofluorescent identified microglia, in coronally sectioned tissues, using ionized calcium-binding adapter molecule-1 (Iba-1) labeling. We used three methods to examine microglia morphology: mean fluorescence intensity, soma volume, and single-cell tracing. For soma volume and single cell tracing, we reconstructed the 3D microglia in the Neurolucida software and analyzed their morphology using Sholl analysis. We used Alternaria alternata in our environmental chamber to model peripheral allergic inflammation. We found that female microglia increase their cell number and nodes while males did not. We conclude that females are more responsive to Alternaria than males, increasing their cell density and surveillance.