Objective: To investigate the changes in 5-HT and substance P in the brain stem of rats with trigeminal neuralgia. Materials and Methods: The animal model of trigeminal neuralgia in rats was established and then measured the concentration of 5-HT and substance P using fluorophotometry and radioimmunological analysis. Results: The concentration of 5-HT in the experimental group was significantly lower than in the normal group (p<0.01). The concentration of substance P in the experimental group was much higher than in control group. Conclusion: The concentration of 5-HT in brain stem was significantly lower in trigeminal neuralgia, while substance P may mediate conduction of nociceptive signals from trigeminal neuralgia.