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The aim of this study was to evaluate the deep convolutional neural networks (DCNNs) based on analysis of cephalometric radiographs for the differential diagnosis of the indications of orthognathic surgery. Among the DCNNs, Modified-Alexnet, MobileNet, and Resnet50 were used, and the accuracy of the models was evaluated by performing 4-fold cross validation. Additionally, gradient-weighted class activation mapping (Grad-CAM) was used to perform visualized interpretation to determine which region affected the DCNNs’ class classification. The prediction accuracy of the models was 96.4% for Modified-Alexnet, 95.4% for MobileNet, and 95.6% for Resnet50. According to the Grad-CAM analysis, the most influential regions for the DCNNs’ class classification were the maxillary and mandibular teeth, mandible, and mandibular symphysis. This study suggests that DCNNs-based analysis of cephalometric radiograph images can be successfully applied for differential diagnosis of the indications of orthognathic surgery.