An algorithm is a "step-by-step procedure for solving a problem or accomplishing some end....in a finite number of steps." (Merriam-Webster, 2009). Medical algorithms are decision trees to help with diagnostic and therapeutic decisions. For the treatment of epilepsy there is no generally accepted treatment algorithm, as individual epilepsy centers follow different diagnostic and therapeutic guidelines. This article presents two algorithms to guide decisions in the treatment of refractory partial epilepsy. The treatment algorithm describes a stepwise diagnostic and therapeutic approach to intractable medial temporal and neocortical epilepsy. The surgical algorithm guides decisions in the surgical treatment of neocortical epilepsy.