Clinical neuroimaging is normal in over 50% of new-onset focal epilepsies, and generally normal in idiopathic generalised epilepsies. How can advanced functional and structural imaging further our understanding of epileptogenesis and cognitive functions in focal and generalised epilepsies, and how might neuroimaging be used in the future to improve surgical outcome, as well as predicting response to medication? Group analyses of functional, structural and effective connectivity based on functional magnetic resonance imaging (fMRI) and diffusion tensor imaging provide evidence for unique anatomical structures that are involved in the modulation of seizure activity, and their role in specific syndromes. Whilst there is evidence that focal seizures arise and are sustained within a network of interconnected brain regions, the deep frontal piriform cortex plays an important role in modulating seizure activity. Altered connectivity with the supplementary motor area may represent the anatomical basis for cognitive triggering of motor seizures in juvenile myoclonic epilepsy. A major challenge for the future use of neuroimaging is the widening of applications beyond ‘surgical imaging’ to include individual predictions of disease progression and of response to medication.