This study was designed to investigate stresses in the TMJ clenching in patients with skeletal discrepancies in the vertical direction. A three-dimensional model of the mandible including the TMJ was used for finite element analysis for the stresses. The model, referred to as a standard model, consists of 2,088 modes and 1,105 solid elements, comprising the cortical and cancellous bones, articular disc and cartilage layer, and periodontal ligament. The standard model was modified by varying the gonial and mandibular plane angles to simulate vertical discrepancies between the maxilla and mandible observed in open and deep bites. Stresses were analyzed on the surfaces of the condule, the glenoid fossa, and the articular disc, and the values were compared to those found with the standard model. Stresses increased substantially for the condule, the glenoid fossa, and the articular disc with greater gonial and mandibular plane angles, and those changes were more obvious in association with the divergent mandibular plane. Thus, the nature of stress distributins in the TMJ was substantially affected by vertical discrepancies of the craniofacial skeleton. It is also suggested that these changes in stresses produce a lack of biomechanical equilibrium in the TMJ, which may have some association with tempromandibular disorders.