The classification of the epilepsies was advanced in order to formalize efforts to identify coherent clinical entities and to develop a standardized set of diagnostic terminology for facilitating communication among workers in the field world-wide. The classification initially was, and still is today, based primarily on description and expert opinion. In the era of genomics, neuroimaging and tremendous technological and scientific advances in the neurosciences, it is time to introduce scientific principles and standards into the classification of the epilepsies. Phylogenetic systematics provides an initial model worth studying in this context. While the classification of species cannot be directly applied to the classification of epilepsy syndromes, three general points can be appreciated. (1) In evolutionary biology, there is an operationalized definition of the end point (a species). There is no such definition of a syndrome. (2) There are rules and criteria for the type of evidence and how it is evaluated to determine whether an entity does or does not represent a separate species. There are currently no such rules or criteria for epilepsy syndromes. (3) There is an underlying model (evolution) that generates the diversity among species. With the possible and only partial exception of the idiopathic generalized epilepsies, there are no models to explain the diversity among the epilepsies. Previously held beliefs and convictions must, in time, give way to dispassionate examination of testable scientific hypotheses examined with rigorously collected scientific evidence. Although current classification is in need of revision, it has also come into common use and has great practical utility. Any changes to its form and to the terminology of the classification must be made only after careful deliberation and broad consensus is reached. The change(s) should be based on agreed upon scientific criteria and processes. Any changes should represent major improvements and not merely incremental steps.