We review the neural mechanisms that support top-down control of behaviour and suggest that goal-directed behaviour uses two systems that work in concert. A basal ganglia-centred system quickly learns simple, fixed goal-directed behaviours while a prefrontal cortex-centred system gradually learns more complex (abstract or long-term) goal-directed behaviours. Interactions between these two systems allow top-down control mechanisms to learn how to direct behaviour towards a goal but also how to guide behaviour when faced with a novel situation.