One of the endocrine glands that play a significant role in the development of the prenatal brain is Thyroid. Therefore, the aim of this study is to compare the levels of BDNF and NGF gene expressions in the brains of male and female babies born on the first day methimazole-induced hypothyroidism Mice with NMRI race. In this study, 30 mature mice of Albino NMRI race were selected. Mice (Albino NMRI) were identified using after mating. In the next stage, we divided mice into three groups (high-dose intervention, low-dose intervention and control groups). Pure water was given during pregnancy to the control group. In the low dose group until the end of pregnancy given 20 mg of methimazole that dissolved in 100 cc of water. Also, in the high-dose group during period pregnancy until the end, they were given 100 mg of methimazole that dissolved in 100 cc of water. After the end of pregnancy, blood samples were taken from the mother's mice to determine the amount of T3 and T4 present in the bloodstream. In the end stage, the brain of one-day mice was removed and to determine the expression of BDNF, NGF we used to RT-PCR. According to the result this study, amount of T4 and T3 in the control group and low dose (27 and 1.59 ng/dl, and 8 and 0.87 ng/dl), respectively indicating a significant reduction in the expression of NT4, NT3, NGF and BDNF gene (P<0.05). Based on result of this study, between the high dose and control group there was significant relationship reduction in the expression (P<0.05).