Historically, alcohol has been used for different purposes including as a part of religious observances, as a food, at times as a medicine and its well-known use as a beverage. Until relatively recently these purposes have not changed and have at times been at odds with one another, resulting in collisions among policies and practices in science, medicine, public policy and the law. One area in which this has been particularly true is that of fetal alcohol spectrum disorders (FASD) where the adverse consequences of consumed alcohol on children in the womb and after birth may have been observed since antiquity, but the actions taken based on such observations have been influenced as much by the socio/cultural/political context of the times in which they were made as by evidence of harm. This article provides an overview of the inherent confusion when new scientific findings confront prevailing medical practice, the history involved in this confusion with respect to FASD, including public policy and legal issues that have arisen around alcohol and pregnancy, and the research and clinical challenges still being faced.