It is well known that thymus gland which is the important organ of the immune system, from its functions in the development of the T cell, and the secretion of the hormones that are responsible for their differentiation to mature T- cells making it the only part of immune system responsible for cell mediated immunity. Objectives: This study performed to explain the effect of alcohol uptake by pregnant mothers on the changes occurred in the neonates thymus both the histological structure, and sugar content (mucopolysaccharides in the tissue, and sialic acid (SA) level (Total Sialic Acid TSA and Lipid Bound Sialic Acid (LBSA)) in homogenated thymuses and correlate the results with the results of he sialic acid level in the serum of the mothers in order to assess accuracy wither the SA as a biological marker for ehhects of alcohol on the thymus of the neonates. Materials and methods: Three groups of pregnant albino mice were used, five females in each, one of the groups was the control group, the other two were administered orally with 0.1 ml ethanol daily with the concentrations of (20 & 30) % for group (2 & 3) respectively from day one of pregnancy until delivery (three weeks). The serum of the mothers were collected for assessing for the TSA and LBSA levels, the thymus of the neonates of each mother were divided into two, half of them went to the to histological studies for different stains with (H&E, PAS reaction for demonstration the mucopolysaccharides and PA* - P- TCH- SP- PD for sialic acid) and study the mitotic index in the thymus cortex, while the other for biochemical studies of the sialic acid level in both the thymus homogenates and the serum of the mothers. Results: the results of the histological study of the neonatal thymus of mothers administrated with (20 & 30) % ethanol showed many changes, decreasing the adipose tissue of the capsule connective tissue, and this damage observed progressively with the increasing concentration of the alcohol, also ethanol in both concentration (20 and 30) % caused damage to the blood barrier in the thymus by disruption in the endothelial cells and surrounding thymic epithelial cells (TECs), at the same time, decrease the amount of the mucopolysaccharides in the tissue of the two groups compared with control group as detected by the PAS reaction with an increase the intercellular spaces, in all regions of the thymus. The mitotic index of the developing thymocytes in the cortex showed a significant decrease (P < 0.05) comparing with control group. Histological results of the amount of SA in situ in thymus tissue was correlated with its level in the thymus homogenate, revealed a significant decrease (P< 0.01) in the (TSA & LBSA) levels in the mice of treated mothers with (20 & 30) % ethanol. Sialic acid of serum of the mothers showed a decrease (P< 0.05) of the level of the TSA and Lipid bound sialic acid (LBSA) in the ethanol treated mother as compared with control group. From these findings it is concluded that the alcohol taken by the mothers during the pregnancy crosses the placental barrier and causes many damage to the thymus tissue and decreases the level of the SA. The decreasing results progressively in the mother and neonates with increasing concentration of alcohol, indicated that the degree of the effect or damage in the neonatal thymus due to the mother uptake dose.