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Cone-beam computed tomographic (CBCT) imaging is useful in detecting apical periodontitis, which is often missed in periapical (PA) radiographs. This study aimed to identify preoperative predictors correlated with the presence of apical periodontitis visible only in CBCT images and to investigate the important characteristics of such lesions.In total, 332 consecutive patients with both PA radiographs and CBCT images were enrolled in this study. The patients’ clinical charts were reviewed retrospectively to collect information regarding their symptoms and diagnoses. Periapical lesions were assessed using a modified CBCT PA index by 2 endodontists. Patient-related factors (age, sex, and symptoms) and tooth-related factors (tooth type, location, pulp status, and pulpal diagnosis) were assessed to determine their relationships with the presence of apical periodontitis visible only in CBCT images.Apical periodontitis was detected in 24.6% and 35.5% of untreated teeth by PA radiographs and CBCT images, respectively. In a multivariate logistic regression analysis, pulp necrosis was significantly correlated with the presence of apical periodontitis visible only in CBCT images (odds ratio = 5.401; 95% confidence interval, 1.911–15.265; P = .001); the involvement of molars showed borderline nonsignificant correlation (odds ratio = 2.843; 95% confidence interval, 0.990–8.164; P = .052). Lesion sizes smaller than 2 mm in diameter and the involvement of molars were significant factors of lesions visible only in CBCT images (P < .05).Pulp necrosis was a preoperative predictor of apical periodontitis visible only in CBCT images. This research could provide a proper indication for CBCT imaging at diagnostic stages.