At weaning, mammals switch from drinking mother's milk to eating foods of environmental origin. These foods contain natural compounds with novel tastes and textures, which are provided to the young for the first time following the termination of breastfeeding. This novel eating experience may alter the cognitive brain function of mammalian babies, increasing their reactions to their food environments. Because the cerebral cortex is a central organ for cognition and learning, we investigated differences in whole-gene expression profiles in the mouse cerebral cortex using microarray analysis before and after weaning. Of 45,037 murine genes, 35 genes were upregulated and 31 genes were downregulated, in response to weaning. In particular, immediate early genes, molecular chaperones, and myelin-related genes were upregulated. In situ hybridization analysis revealed that the mRNA for an immediate early gene, Egr-2/KROX-20, was transported from the nucleus to the cell body at layer 5/6 of the somatosensory cortex during weaning. In contrast, in animals without any food supply other than mother's milk, Egr-2/KROX-20 mRNA was retained within the nucleus at the somatosensory cortex. These data suggest that the novel experience of food intake modulates gene expression profiles in the murine cerebral cortex at the weaning stage. (C) 2013 Elsevier Inc. All rights reserved.