Purpose: This study is to evaluate the location of descending palatine artery, the anatomy of pterygomaxillary junction, and the association between the obtained anatomic values and several variables. Methods: We studied 40 patients who were treated for dentofacial deformites from January 2010 to December 2012 in Ulsan University Hospital, Ulsan, Korea. Cone beam computed tomogram (CBCT) was done for all patients. The reference point was approximately 5 to 7 mm above anterior nasal spine on axial image. We evaluated the location of the greater palatine canal (line a: on the coronal view, the shortest line between the center of greater palatine canal and pterygoid fossa; distance a: the distance of line a). We also measured the thickness (line b: on the coronal view, the shortest line between maxillary posterior sinus wall and pterygoid fossa; distance b: distance of line b), width (line c: on the coronal view, the line perpendicular to the line b and the nearest line from the most concave point of lateral pterygoid plate to the medial pterygoid plate; distance c: distance of line c) and height (line d: on sagittal view, the vertically longest line of pterygoid junction; distance d: the distance of line d) in pterygomaxillary junctions. We evaluated the association between the obtained anatomic values and several variables (sex, age, height and weight). Results: The mean distance a was 4.78 mm, mean distance b was 5.53 mm, mean distance c was 8.01 mm and mean distance d was 13.22 mm. The differences between age and mean distance c and weight and mean distance d in pterygomaxillary junctions are statistically significant. Conclusion: There apparently is anatomic variation of pterygomaxillary junctions by various values, particularly weight and age in a Korean clinical population.