We have recently demonstrated that prenatal exposure to the histone deacetylase (HDAC) inhibitor valproic acid (VPA) at embryonic day 12.5 (E12.5) causes autism-like behavioral abnormalities, such as social interaction deficits, anxiety-like behavior and spatial learning disabilities, in male mouse offspring (Int. J. Neuropsychopharamacol., 2013). We have also found that the prenatal VPA exposure causes a transient increase in acetylated histone levels in the embryonic brain, followed by an increase in apoptotic cell death in the neocortex and a decrease in cell proliferation in the ganglionic eminence, and it decreases Nissl-positive cell numbers in the prefrontal and somatosensory cortices after birth. Here, we examined the effect of prenatal exposure to HDAC inhibitors on neuronal maturation. VPA (500 mg/kg, i.p.), trichostatin A (TSA; 500 μg/kg, i.p.) or vehicle was injected into pregnant mice on gestational days 12.5 or 14.5, and primary neurons were prepared from the cerebral cortex at embryonic day 16. Prenatal exposure to VPA at E12.5, but not at E14.5, caused decreases in total numbers and length of neuronal dendrites at 14 days in vitro (14 DIV). The differences disappeared at 21 DIV. Similar delay of cellular maturation was observed in cortical neurons from embryos exposed to TSA at E12.5. Furthermore, the present study demonstrated that the prenatal exposure to HDAC inhibitors at E12.5 decreased neuroligin-1 mRNA level and increased CNTNAP2 and Shank3 mRNA levels. These findings suggested that prenatal exposure to HDAC inhibitors at E12.5 delays neuronal maturation by regulating gene expression of morphogenesis-related molecules.