An holistic theory of the functional organization of the central nervous system, a system at the level of the organ, in vertebrate organisms is presented as an alternative to localization of function by using two sets of complementary rules for systems designation derived from systems theory. These rules reveal three types of systems according to levels of operation and the origins of goals. These are: (1) the teleogenic or primary systems (reproductive, food-water intake-use, thermoregulative, immune, oxygen intake-use); (2) the teleozetic or subsystems (internal sensory and motor, external motor, external sensory); (3) the teleonomic systems or echelons (field, local circuit, basic functional unit, basic excitation unit). The systems, subsystems, and echelons are discussed with regard to their hierarchical relationships, the nature of their goals, and the supporting experimental evidence. The theory is discussed as an explicit statement of multileveled relationships for the analysis of the vertebrate CNS and, therefore, as presenting a paradigm for, or a way of thinking about, local and global brain theories, brain dysfunction, and brain evolution.