Possible mechanisms of the interactions of neuron functioning in the connectome including topographically connected areas of the neocortex, hippocampus, basal ganglia, cerebellum, thalamus, and the various CNS nuclei connected with them are analyzed. These mechanisms are based on published results from morphological and electrophysiological studies, previously formulated unified rules for the modification and modulation of the efficiency of synaptic transmission, as well as the results of previous analyses of the features of the functioning of the hippocampal formation, cerebellum, and neural cortico-basal ganglia-thalamocortical loops. The cerebellum influences the neocortex and basal ganglia via topographically connected thalamic nuclei. The cerebellum can influence the functioning of the hippocampus via the thalamic reuniens nucleus and the retrosplenial and prefrontal areas of the cortex, the medial septum, and the supramammillary nucleus. The hippocampus can influence cerebellar functioning via the neocortex and pontine nuclei, as well as via the basal ganglia, the targets of whose output nuclei are the subthalamic nucleus and the pedunculopontine nucleus. The basal ganglia, cerebellum, and subthalamic nucleus influence motor activity via the red nucleus. Considering the topographic organization of connections between structures, we suggest that the brain can be regarded as a global connectome consisting of separate but similarly organized connectomes, each taking part in processing a particular type of information. The mechanisms of the functioning of these connectomes are uniform. This analysis of the mechanisms of the interacting functioning of neurons in the connectome is of interest for understanding the mechanisms of the functioning of the global connectome, where processing of sensory information of different modalities, its perception, and selection of the appropriate response all take place. It is presumed that the default mode network of the brain, which includes the higher areas of the neocortex, is the part of the global connectome operating in the resting state. Comparison of the mechanisms of the functioning of each connectome in normal conditions and pathology should provide for assessment of current methods for the treatment of neurological diseases and facilitate the targeted search for new treatment methods. © 2022, Springer Nature Switzerland AG.