Microglia play a dual role in neuroprotection as well as in neurodegeneration and thus occupy the focal interest in neurodegenerative disease research. In vitro studies either by using cell lines or neonatal mouse primary microglia correlated xenobiotic induced microglial activation and neuronal death. However, these in vitro studies cannot portray the in vivo scenario. Therefore, environmental pollutant induced in vivo alteration in microglial function can be best assessed by ex vivo analysis, which is not in use because of limitations in the isolation procedure. Therefore, in the first part of the study we describe an optimized isolation procedure and characterization of isolated cells. The second part of the study demonstrates the utility of the isolated cells in evaluation of immunotoxicological alterations following arsenic, as a model xenobiotic, exposure. Purity of the isolated microglia was checked by immunostaining of microglial (CD11b and CD68) and nonmicroglial (GFAP) markers. Immunostaining of activation marker Iba1 proves that cells were not activated during the isolation procedure. Microglia yield and viability from the treated group shows no significant alterations compared to that of the control group. Proinflammatory cytokines (IL-6 and TNF-α) were upregulated following arsenic treatment as in the case of the LPS stimulated group without alterations in anti-inflammatory IL-10. Phagocytic potential was affected significantly following arsenic exposure without alteration in viability. Thus, our protocol can be proficiently used for quick isolation of primary microglia from adult mouse brain without altering their activation status, and most importantly, the isolated cells can be of aid to the ex vivo evaluation of immunotoxicological alterations.