Upon prolonged alcohol exposure, the behaviour of an individual can gradually switch from controlled to compulsive. Our review is focused on the neurobiological mechanisms that might underlie this transition as well as the factors that are influencing it. Animal studies suggest that temporally increased alcohol consumption during post-abstinence drinking is accompanied by a loss of flexibility of the behaviour and therefore, could serve as a model for compulsive alcohol drinking. However, studies using different alcohol-preferring rat lines in the post-abstinence drinking model suggest that high alcohol consumption does not necessarily lead to the development of compulsive drinking. This indicates the significance of genetic predisposition to compulsive behaviour. Neuroimaging data show that chronic alcohol consumption affects the activity of several brain regions such as the extrapyramidal motor system and several areas of the prefrontal cortex including the orbitofrontal and anterior cingulate cortex. Similar changes in brain activity is seen in patients suffering from obsessive-compulsive disorder at baseline conditions and during provocation of obsessive thoughts and urge to perform compulsive-like rituals. This indicates that dysfunction of these regions may be responsible for the expression of compulsive components of alcohol drinking behaviour. Several brain neurotransmitter systems seem to be responsible for the switch from controlled to compulsive behaviour. In particular, hypofunctioning of monoaminergic systems and hyperfunctioning of glutamatergic systems may play a role in compulsive alcohol drinking.