Alcohol-use disorders (AUDs) are a major public health concern in the United States. To better understand the etiology of alcohol dependence and to identify physiological and behavioral markers that predict alcohol use progression, research has focused on linking diagnostic phenotypes with genetic variation. In recent years, neurobiological endophenotypes have largely surpassed clinical symptoms as the major phenotypes of interest, because they are typically more proximal to underlying genetic mechanisms, and can help to fill the gaps between genetic variation and clinical diagnosis. To date, numerous useful neurobiological endophenotypes for alcohol dependence have been uncovered, including those related to reward dysregulation, impulsivity, and subjective response to alcohol, In general, further work is needed to demonstrate direct associations between AUD endophenotypes and specific genetic variation. Future research would also benefit from applying a theoretical framework emphasizing the shifting imbalance between reward and control networks that occurs during the typical progression from recreational drinking to alcohol dependence. Identifying endophenotypes characteristic of different stages of addiction could have important diagnostic and treatment implications.