Purpose: The individual jaw position is determined by the masticatory muscle among other factors. Before surgical treatment of malocclusions, thorough evaluation of the muscles is required to estimate the relapse risk. Materials and Methods: By means of computer tomography, lateral radiographs of the skull and denture models, the relationships between morphological parameters of the masticatory muscles and the jaw bone were analyzed. Furthermore, possible causes for the extent of the malocclusion are described. Results: A patient group with deep overbite was found to have significantly higher muscle densities (measured in Hounsfield units [HU]) in the medial pterygoideus muscle (59.89 ± 3.91 HU to 48.94 ± 4.14 HU, p < 0.01), masseter muscle, and genioglossus muscle (p < 0.05) in comparison to open bite patients. Significant differences of the muscle cross-section were measured in the masseter muscle between patients with retroclined maxillary incisors and with an open bite (5.4 ± 0.7 cm² to 3.8 ± 0.4 cm², p < 0.05). Conclusion: The results show a correlation between different jaw positions and masticatory muscles. They also suggest that the function of each muscle may be different. Additional examinations of the muscle structures are required for verification of the influence of the masticatory muscles on facial morphology.