The study of the formation of neuronal maps in the brain has greatly increased our understanding of how the brain develops and, in some cases, regenerates. Computational modeling of neuronal map development has been invaluable in integrating complex biological phenomena and synthesizing them into quantitative and predictive frameworks. These models allow us to investigate how neuronal map development is perturbed under conditions of altered development, disease and regeneration. In this article, we use examples of activity-dependent and activity-independent models of retinotopic map formation to illustrate how they can aid our understanding of developmental and acquired disease processes. We note that fully extending these models to specific clinically relevant problems is a largely unexplored domain and suggest future work in this direction. We argue that this type of modeling will be necessary in furthering our understanding of the pathophysiology of neurological diseases and in developing treatments for them. Furthermore, we discuss how the nature of computational and theoretical approaches uniquely places them to bridge the gap between the bench and the clinic.