Some craniofacial diseases or anatomical variations are found in radiographic images taken for other purposes. These incidental findings (IFs) can be detected in orthodontic patients, as various radiographs are required for orthodontic diagnosis. The radiographic data of 1020-orthodontic patients were interpreted to evaluate the rates of IFs in three-dimensional (3D) cone-beam-computed tomography (CBCT) with a large field of view (FOV) and investigate the effectiveness and accuracy of two-dimensional (2D) radiographs for detecting IFs compared to CBCT. Prevalence and accuracy in five areas was measured for sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). The accuracies of various 2D-radiograph were compared through a proportion test. A total of 709-cases (69.5%) of 1020-subjects showed one or more IFs in CBCT images. Nasal cavity was the most affected area. Based on the CBCT images as a gold standard, different accuracies of various 2D-radiographs were observed in each area of the findings. The highest accuracy was confirmed in soft tissue calcifications with comprehensive radiographs. For detecting nasal septum deviations, postero-anterior cephalograms were the most accurate 2D radiograph. In cases the IFs were not determined because of its ambiguity in 2D radiographs, considering them as an absence of findings increased the accuracy.