The autonomic nervous system plays a major role in metabolism regulation by modulating metabolic pathways directly or indirectly via control of hormone (particularly insulin) secretion in various organs and tissues. In addition, the system modulates the proliferation and differentiation of some cell types. This activity is directly controlled by certain brain areas, particularly those located in the hypothalamus. A feedback loop signals metabolic changes at the periphery to these brain areas. This review focuses on the role of the autonomic nervous system in the activity and plasticity of pancreas and adipose tissues under normal conditions or in obesity, with special attention to the importance of alterations in these functions.