Sub-cortical grey matter structures, such as the putamen, pallidum, caudate, thalamus, amygdala and hippocampus, play substantial roles in both simple and complex brain functions, including regulation of pleasure and emotions; control of movements; learning; decision-making; language development; and sensory, cognitive, social and other higher-order functions. Most of these regions act as information hubs for the nervous system, relaying and controlling the flow of information to various portions of the brain. To further understand the complex neurophysiological characteristics of sub-cortical areas, the aim of this study was to investigate the functional integrations of six sub-cortical areas to different major functional brain networks. One hundred ninety-eight healthy individuals were examined using resting-state functional MRI. The seeds identified in this study were six sub-cortical deep grey matter regions, namely putamen, pallidum, caudate, thalamus, amygdala and hippocampus. The analysis indicated that the link between the sub-cortical regions and some functional brain networks was similar in some aspects, but there were disparities in the mechanism underlying such a link and in the existence of functional connections between these regions and networks. Despite the substantial functional connectivity linkages between the sub-cortical regions, discrepancies were still noted. On the basis of the connections to the majority of the major brain networks, this study demonstrated the essential functional roles and involvements of the sub-cortical regions. This finding is consistent with an earlier report that revealed a substantial role of the sub-cortical regions in several brain functions.