Aims: To specify the regions of the brain stem that are characterized by changes in substance P (SP)-like immunoreactivity following activation of capsaicin-sensitive afferents innervating temporomandibular joint (TMJ) tissues in New Zealand rabbits. Methods: Capsaicin, an activator of small-diameter unmyelinated and thinly myelinated nociceptive afferent fibers, was administered unilaterally to the right TMJ of experimental animals. Another group received vehicle solution and served as controls. The animals were sacrificed 6 hours post-treatment through transcardial perfusion. Their brain stems were removed and sectioned, and SP-like immunoreactivity was assessed in serial horizontal sections. Results: A decrease in brain stem SP-like immunoreactivity occurred ipsilateral to capsaicin application. This reduction was primarily localized in brain stem regions that correspond to the trigeminal main sensory nucleus, as well as subnucleus oralis, interpolaris, and caudalis of the trigeminal spinal tract nucleus. Conclusion: The present study revealed central nervous system changes following TMJ capsaicin treatment in rabbits.