Introduction: This investigation was undertaken to examine the influence of thyroid hormone on the development of embryonic CNS during embryogenesis pattern and compare the microscopical and macroscopical structure of the brain in the control and experimental fetuses. Materials and method: 40 Rats, made hypothyroid by chemical thyroidectomy with (PTU). Three weeks later, after T4 and TSH examination, hypothyroid rats mated with euthyroid male rats. Therefore the fetuses of E14, E16 and E20 were collected in two groups as exprimental and control then macroscopical and microscopical studies were carried out. Brain sections with thickness of 10-15mm were pared and stained with H&E and Alcian blue with critical electrolyte concentration with four concentration cations, of Mg. Results: Significant differences were seen in body and brain weight, and Crown Ramp (CR) of embryos in hypothyroid groups. In hypothyroid pregnant rats, it has been reported to cause fetal growth retardation and in this study stillborns, spontaneous abortion and miscarriage were observed in hypothyroid dams. Significant changes in thickness of different layers of pallium and specially in plexiform layer were seen. Thickness of pallium in hypothyroid fetuses in E14 and E16 shows significant difference with P<0.005. Conclusion: It seems that maternal hypothyroidism has an effect on the number of fetuses per dams, and unstability of pregnancy, also the increase of abortion and absorbtion of fetuses may be due to the decrease in the level of serum T4 of the pregnant dams. There is evidence that thyroid hormone in fluences the neuronal development of vertebrate. Thyroid hormone deprivation may delay acquisition of the normal number of cells and abnormal maturation of cerebellar cells.