The cerebral nuclei form the ventral division of the cerebral hemisphere and are thought to play an important role in neural systems controlling somatic movement and motivation. Network analysis was used to define global architectural features of intrinsic cerebral nuclei circuitry in one hemisphere (association connections) and between hemispheres (commissural connections). The analysis was based on more than 4,000 reports of histologically defined axonal connections involving all 45 gray matter regions of the rat cerebral nuclei and revealed the existence of four asymmetrically interconnected modules. The modules form four topographically distinct longitudinal columns that only partly correspond to previous interpretations of cerebral nuclei structure-function organization. The network of connections within and between modules in one hemisphere or the other is quite dense (about 40% of all possible connections), whereas the network of connections between hemispheres is weak and sparse (only about 5% of all possible connections). Particularly highly interconnected regions (rich club and hubs within it) form a topologically continuous band extending through two of the modules. Connection path lengths among numerous pairs of regions, and among some of the network's modules, are relatively long, thus accounting for low global efficiency in network communication. These results provide a starting point for reexamining the connectional organization of the cerebral hemispheres as a whole (right and left cerebral cortex and cerebral nuclei together) and their relation to the rest of the nervous system. behavior | connectomics | mammal | neural connections | neuroinformatics T he paired adult vertebrate cerebral hemispheres are differentiations of the embryonic neural tube's endbrain (telencephalic) vesicle, which in turn forms a ventral nonlaminated part, the cerebral nuclei, and then a dorsal laminated part, the cerebral cortex (1-3). In mammals the largest parts of the cerebral nuclei by volume are the caudoputamen (striatal) and globus pallidus (pallidal). Together, they are commonly regarded as the endbrain parts of the basal ganglia (3), which play an important role in controlling skeletomuscular (somatic) movements and in the etiology of movement disorders (4).A major shift in thinking about the basal ganglia occurred with the recognition that certain ventral parts of the cerebral nuclei display the same basic circuit organization, but involve different parts of a cerebral cortex to cerebral nuclei to thalamus to cerebral cortex loop (5). This finding led to an expanded view of the basal ganglia, with dorsal and ventral striatopallidal subsystems involved primarily in movement (dorsal) and motivational functionality (ventral) (6). Complete expansion of the view was then proposed on the basis of connectional, gene expression, embryological, and functional evidence (7). It was hypothesized that the entire cerebral cortex, cerebral nuclei, and thalamus can be divided into four basic subsystems involving dorsal, vent...