Neuro developmental diseases are often associated with viral infection during pregnancy. In mice, Maternal Immune Activation (MIA) results in cognitive and social abnormalities of the offspring at adulthood. However, the underlying mechanism is still not fully understood. Here we hypothesized that prenatal immune challenge might impact the developing microglia, which thereby perturbs the normal brain development. To test this hypothesis, we treated pregnant dams with the viral mimetic poly(I:C), as the prenatal inflammatory stimuli, 14.5days following gestation, and compared the microglia isolated from their offspring, to microglia isolated from offspring of PBS treated pregnant controls. Using high-throughput mRNA sequencing and gene ontology analysis, we found a reduction in expression of genes related to proliferation and cell cycle in the microglia isolated from newborn offspring of poly(I:C) injected dams, compared to offspring of PBS-treated dams, which was confirmed by flow cytometry analysis, assessing microglial expression of the proliferation marker Ki67. Moreover, examination of embryonic yolk sac, the origin of microglia in the developing offspring, showed a signature of the maternal poly(I:C) treatment, compared to the control samples. Our results suggest that immune activation during pregnancy interferes with the microglia programmed development cascade, which are manifested at adulthood in brain dysfunctions associated with neuro developmental diseases.