Basic biomedical knowledge of the neurobiological mechanisms of the deafferentation of stomatognathic systems has expanded greatly in recent decades. In both human and animal experimental trials, there are indications that the deafferentation of stomatognathic systems may be a critical factor in triggering and aggravating neurodegenerative diseases. This review explores basic neurobiological mechanisms associated with the deafferentation of stomatognathic systems; further included is a discussion on tooth loss and other oral-maxillofacial deafferentation (OMFD) mechanisms, with a focus on dental and periodontal apparatus that are associated with brain function and that may underlie the changes observed in the aging brain. A new hypothesis is proposed that tooth loss and changes in the functionality of teeth may cause brain damage due to recurrent remapping of the brain, and may even be a triggering and aggravating factor in the onset and progression of Alzheimer's disease. A growing understanding of the association of OMFD with brain aging may lead to solutions in treating and preventing cognitive decline and Alzheimer's disease.