Objectives: The purpose of this study was to automatically diagnose odontogenic cysts and tumors of both jaws on panoramic radiographs using deep learning. We proposed a novel framework of deep convolution neural network (CNN) with data augmentation for detection and classification of the multiple diseases. Methods: We developed a deep CNN modified from YOLOv3 for detecting and classifying odontogenic cysts and tumors of both jaws. Our data set of 1282 panoramic radiographs comprised 350 dentigerous cysts (DCs), 302 periapical cysts (PCs), 300 odontogenic keratocysts (OKCs), 230 ameloblastomas (ABs), and 100 normal jaws with no disease. In addition, the number of radiographs was augmented 12-fold by flip, rotation, and intensity changes. We evaluated the classification performance of the developed CNN by calculating sensitivity, specificity, accuracy, and area under the curve (AUC) for diseases of both jaws. Results: The overall classification performance for the diseases improved from 78.2% sensitivity, 93.9% specificity,91.3% accuracy, and 0.86 AUC using the CNN with unaugmented data set to 88.9% sensitivity, 97.2% specificity, 95.6% accuracy, and 0.94 AUC using the CNN with augmented data set. CNN using augmented data set had the following sensitivities, specificities, accuracies, and AUCs: 91.4%, 99.2%, 97.8%, and 0.96 for DCs, 82.8%, 99.2%, 96.2%, and 0.92 for PCs, 98.4%,92.3%,94.0%, and 0.97 for OKCs, 71.7%, 100%, 94.3%, and 0.86 for ABs, and 100.0%, 95.1%, 96.0%, and 0.97 for normal jaws, respectively. Conclusion: The CNN method we developed for automatically diagnosing odontogenic cysts and tumors of both jaws on panoramic radiographs using data augmentation showed high sensitivity, specificity, accuracy, and AUC despite the limited number of panoramic images involved.