Perfluorooctane sulfonate (PFOS), a persistent and bioaccumulative compound, is widely distributed in the environment. To explore the molecular mechanism of neonatal neurotoxic effects, we evaluated the transcriptional effects of prenatal and neonatal exposure to PFOS in developing rat brain by performing gene expression profiling in the cerebral cortex. Dams received 3.2 mg/kg PFOS in their feed from gestational day 1 (GD1) to weaning (PND 21). Pups then had free access to treated feed until PND 35. Six Illumina RatRef-12 Expression BeadChips were used to identify gene expression changes on postnatal days (PNDs) 1, 7, and 35. Significantly affected genes (P < 0.05) were involved in neuroactive ligand-receptor interaction, calcium signaling pathways, cell communication, long-term potentiation/depression, the cell cycle, and peroxisome proliferator-activated receptor (PPAR) signaling. To compare prenatal and lactational exposure contributions to transcriptional effects, a subset of altered genes obtained from the gene-profile study that represented neurobiological functions was analyzed using RT-PCR in a follow-up cross-foster study lasting from PND1 to 21. Prenatal and postnatal exposure to PFOS caused potential neurotoxicity as demonstrated by developmentally different global transcriptional changes. Prenatal exposure was more effective in altering expression of several genes. Also, transcriptional effects of PFOS exposure on neurodevelopment occurred primarily by disrupting the neuroendocrine system.