Infectious and inflammatory processes during pregnancy in women provoke maternal immunity activation (MIA) and increase the risk of neuropsychiatric disorders in children. These disorders can lead to neurodegenerative diseases later in life. To study these effects, we evaluated the morphological and molecular biological changes in the hippocampus and prefrontal cortex of male and female Wistar rats on the 1st day of postnatal ontogenesis after LPS-induced MIA. The level of calprotectin in the blood serum of postpartum rats, the number and morphological properties of microglial cells in the hippocampus, and the expression of proinflammatory, stem, and adaptation markers in fragments of the prefrontal cortex in offspring of both sexes were determined. It was found that LPS-induced MIA had a negative effect on the developing offspring, with an increase in the level of expression of Nfκb and App in the prefrontal cortex of newborns being observed. Sex differences in morphological and molecular biological changes in the brains of newborn Wistar rats were also revealed: the number of microglial cells increased in male rats, while the number of ramified microglial cells decreased in female rats. In addition, only in females, the expression levels of the mRNA markers for stem cells, Sox2 and Sox9, decreased, while the expression level of Hif1α, which has a neuroprotective effect, increased only in males. These data may explain the differences in the incidence of neurodegenerative diseases among elderly patients of different sexes. © 2025 Elsevier B.V., All rights reserved.