Formation of tissues and organs during development and regeneration is a highly complex process that comprises diverse local interactions at the molecular and cellular levels, yet mechanisms that integrate biological subunits (e.g., cells) into coherently functioning units or systems (e.g., cell circuits or tissues) are not well understood. Self-organization is a phenomenon where lower level components of a system produce a global architecture or pattern through various local interactions without referring to an inclusive “blueprint” of the final structure. Understanding governing principles of self-organization at the cellular level can provide fundamental insights to various stages of development and maturation of biological systems, such as formation, selective growth and pruning of neuronal circuits as well as acquisition of shape and function. Previous research has shown self-organization of highly complex structures, such as the developing eye using embryonic stem cells grown in a culture environment and with in vivo models focused on ectopic formation of complex structures in various model organisms. However, an experimental approach to study self-organization in its natural setting has been lacking. The planarian eye and the brain offer an unparalleled testing ground as an experimental model to study self-organization. Here, I will present our efforts towards developing a model, involving self-organization and attraction of progenitors into neural circuits, that explains key attributes of nervous system regeneration.