Accuracy in orthognathic surgery with virtual planning has been reported, but detailed analysis of accuracy according to anatomic location, including the mandibular condyle, is insufficient. The purpose of this study was to compare the virtual plan and surgical outcomes and analyze the degree and distribution of errors according to each anatomic location. This retrospective cohort study evaluated skeletal class III patients, treated with bimaxillary surgery. The primary predictor was anatomic locations that consisted of right and left condyles, maxilla, and the distal segment of the mandible. Other variables were age and gender. The primary outcome was surgical accuracy, defined as mean 3-dimensional distance error, mean absolute error, and mean error along the horizontal, vertical, and anteroposterior axes between the virtual plan and surgical outcomes. Landmarks were compared using a computational method based on affine transformation with a 1-time landmark setting. The mean errors were visualized with multidimensional scattergrams. Bivariate and regression statistics were computed. This study included 52 patients, 26 men and 26 women, with a mean age of 21years and 3months. The mean 3D distance errors for condylar landmarks, maxillary landmarks, and landmarks on the distal segment of the mandible were 1.03, 1.25, and 2.24mm, respectively. Condylar landmarks, maxillary landmarks, and the landmarks on the distal segment of the mandible were positioned at 0.49mm inferior, 0.28mm anterior, and 1.25mm inferior, respectively. The landmark errors for the distal segment of the mandible exhibited a wider distribution than those for condylar and maxillary landmarks. Agreement between the planned and actual outcome aided by virtual surgical planning was highest for the condyles, followed by the maxilla, and the distal segment of the mandible. It is important to consider the tendency for surgical errors in each anatomic location during operations.