Currently, the dominating approach to studying functional brain organization is based on the so-called activation studies, in the frameworks of which the functional specializations of different brain structures in the context of studied nature of activity are specified according to their energy states. The concept of organization of brain systems is formed largely thanks to such activation research. However, our studies devoted to the analysis of functional relations between different nodes of the brain systems show that they are much more complicated than they are presented in the activation studies. The structure of brain systems is not limited to those elements that are involved in its work by changing their local neuronal activity. This fact dramatically changes our views on how the brain systems are organized.