Teratogenic effect of alcohol has been documented and maternal alcohol abuse during gestation can result in various fetal injuries. The developmental defects from alcohol abuse during gestation have been described, but it is still unanswered about what are the specific mechanisms by which alcohol mediates these injuries. This is important question to address in order for us to identify affected children at an early age and intervene to prevent or mitigate the damage. Due to the inherent limitations of studies conducted in humans, the use of alternative models is important in addressing these unanswered questions. Embryonic stem cells and adult stem cells have been used as study models to unveil molecular and cellular mechanisms in various signaling pathways. They are especially beneficial to developmental studies where in vivo molecular/cellular study models are not available. This report has demonstrated the adverse effect of EtOH on the gene expression signatures in hESCs that are potentially elicited through epigenetic alterations. We have further profiled genome-wide DNA methylomic marks that are affected by EtOH in hESCs. Our understanding on the effect of alcohol on stem cells will be beneficial to design future clinical application of stem cells to improve human health.