BackgroundIn stroke, functional neuroimaging has become a potent diagnostic tool; opened new insights into the pathophysiology of ischaemic damage in the human brain; and made possible the assessment of functional–structural relationships in postlesion recovery.Summary of reviewHere, we give a critical account on the potential and limitation of functional neuroimaging and discuss concepts related to the use of neuroimaging for exploring the neurobiological and neuroanatomical mechanisms of poststroke recovery and neurorehabilitation. We identify and provide evidence for five hypotheses that functional neuroimaging can provide new insights into: adaptation occurs at the level of functional brain systems; the brain–behaviour relationship varies with recovery and over time; functional neuroimaging can improve our ability to predict recovery and select individuals for rehabilitation; mechanisms of recovery reflect different pathophysiological phases; and brain adaptation may be modulated by experience and specific rehabilitation. The significance and application of this new evidence is discussed, and recommendations made for investigations in the field.ConclusionFunctional neuroimaging is an important tool to explore the mechanisms underlying brain plasticity and, thereby, to guide clinical research in neurorehabilitation.