Autonomy, the ability to make decisions for ourselves about ourselves, is among the most prized of human liberties. In this review we reconsider the key conditions necessary for autonomous decision making, long debated by moral philosophers and ethicists, in light of current neuroscientific evidence. The most widely accepted criteria for autonomy are that decisions are made by a rationally deliberative and reflective agent and that these decisions are free of undue external influences. The corpus of neuroscientific data suggest that human brains are capable of the hierarchical control required for reflective thought, but that decisions conventionally perceived as autonomous may not be rational with respect to the deliberative process itself, and are rarely free from covert external influences. These findings cast doubt upon the capacity for autonomy as traditionally defined, and suggest that we reconsider valorizing the right to autonomy in order to align our moral values with neuroscientific naturalism.