Background The purpose of this study was to assess the cortical-level sensory differences between natural teeth with a periodontal membrane and dental implants. Material and Methods We used functional near-infrared spectroscopy (fNIRS) to measure brain activity in the cerebral cortex of 12 patients who had both natural teeth and dental implants in the lower molar region. Painless vibratory tactile stimulation was performed on both the natural teeth and the dental implants. Results Activation was seen in the somatosensory cortex during stimulation of both natural teeth and dental implants. A comparison of cortical activation showed no significant differences between natural teeth and dental implants. Conclusions These results indicate the possible existence of sensory input to the cerebral cortex via dental implants as well as natural teeth, and thus suggest that may not only the periodontal membrane be involved in the signaling pathway. The data from this experiment may help us for understanding the neural mechanisms underlying natural teeth and dental implants. Key words: fNIRS, natural teeth, implants, brain activity, somatosensory cortex.