Hematopoesis is a proces of new blood cell formation. Transcription factors from the Ikaros and Notch families play a crucial role in lymphocyte development. Ikaros family transcription factors are Ikaros, Aiolos, Helios, Eos and Pegasus. The expression of these factors as well as the Notch signaling pathway is limiting for hematopoietic and lymphocyte development. Due to their importance Ikaros and Notch are highly homologous between species. In this work we show for the first time the expression of Ikaros family transcription factors, Aiolos, Eos and Pegasus in the rat thymus. We also analyzed the rat thymus for Hes expression, a protein which is activated downstream of the Notch signaling pathway. It has been previously shown that ethanol can influence hematopoietic development. Therefore we analyzed the thymus of adult rats whose mothers during gestation drunk 10% ethanol in their drinking water. By four colour flow cytometry we studied the distribution of the major lymphocyte subpopulations in the rat thymus according to CD3, CD4 and CD8 expression. We found a higher incidence of CD3 positive cells in the double positive CD4+CD8+ thymic subpopulation of rats prenatally exposed to ethanol when compared to controls. Further, we established a semi-quantitative RT-PCR in order to detect possible changes in thymus mRNA expression levels of Aiolos, Eos, Pegasus and Hes in rats prenatally exposed to ethanol. A housekeeping gene, HPRT was used as a standard. Rats prenatally exposed to ethanol show a slightly higher expression of Aiolos, Eos, Pegasus and Hes in the thymus when compared to control rats. However these differences were not statisticaly significant. Our findings indicate that ethanol exposure of pregnant rats might influence the developmnet of CD3 positive cells in the thymus which is related to an increase in transcription factor expression.