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Abstract Background Craniofacial disharmony in cases of jaw deformity associated with abnormal lateral deviation of the jaw mostly involves both the maxilla and mandible. However, it has been still difficult to capture the jaw deviation aspect in a 3-dimensional and quantitative techniques. In this study, we focused on 3-dimensional mandibular morphology and position of the condylar head in relation to the base of the skull in patients with mandibular prognathism, one of the most common jaw deformities. We used cluster analysis to quantify and classify deviation and clarified its characteristics. We also investigated the degree of correlation between those findings and menton (Me) deviation measured on frontal cephalograms, which is a conventional indicator of jaw deformity. Results Findings obtained from 100 patients (35 men, 65 women) were classified into the following three groups based on mandibular morphology and condylar position relative to the skull base. Then, reclassification using these parameters enabled classification of cluster analysis findings into seven groups based on abnormal jaw deviation characteristics. Comparison among these seven groups showed that the classification criteria were ramus height, mandibular body length, distance from the gonion to the apex of the coronoid process, and the lateral and vertical positions of the mandible. Weak correlation was also found between Me deviation on frontal cephalograms and each of the above parameters measured on 3D images. Conclusions Focusing on mandibular morphology and condylar position relative to the skull base in patients with mandibular prognathism, we used cluster analysis to quantify and classify jaw deviation. The present results showed that the 3D characteristics of the mandible based on mandibular morphology and condylar position relative to the skull base can be classified into seven groups. Further, we clarified that Me deviation on frontal cephalograms, which has been used to date, is inadequate for capturing jaw deviation characteristics.