Around a third of patients with epilepsy have refractory epilepsy; that is, they continue to have seizures despite trying a range of antiepileptic drugs. Recent basic research has explored the underlying causes of refractory epilepsy, and in this article Sanjay Sisodiya discusses the two main hypotheses that have emerged from these studies. He also considers how knowledge of the molecular basis of refractoriness might guide the development of new therapies.