The recent revision of the classification of the epilepsies released by the ILAE Commission on Classification and Terminology (2005–2009) has been a major development in the field. Papers in this section of the special issue were charged with examining the relevance of other techniques and approaches to examining, categorizing and classifying cognitive and behavioral comorbidities. In that light, we investigate the applicability of graph theory to understand the impact of epilepsy on cognition compared to controls, and then the patterns of cognitive development in normally developing children which would set the stage for prospective comparisons of children with epilepsy and controls. The overall goal is to examine the potential utility of other analytic tools and approaches to conceptualize the cognitive comorbidities in epilepsy. Given that the major cognitive domains representing cognitive function are interdependent, the associations between the neuropsychological abilities underlying these domains can be referred to as a cognitive network. Therefore, the architecture of this cognitive network can be quantified and assessed using graph theory methods, rendering a novel approach to the characterization of cognitive status. In this article we provide fundamental information about graph theory procedures, followed by application of these techniques to cross-sectional analysis of neuropsychological data in children with epilepsy compared to controls, finalizing with prospective analysis of neuropsychological development in younger and older healthy controls.