Objective This study aimed to investigate the diagnostic and differential diagnostic utility of cone beam computed tomography (CBCT) and immunohistochemical staining in distinguishing among periapical cysts, periapical granulomas, and odontogenic keratocysts. Methods The clinicopathological and imaging data of 143 patients with periapical cysts and 45 patients with periapical granulomas were collected and analyzed. A total of 29 cases of paraffin-embedded periapical cysts and 24 cases of odontogenic keratocysts were selected. Immunohistochemical stai-ning for CK14, CK19, CD57, and Ki-67 was performed, and the relevant literature was reviewed. Results The accuracy of CBCT in the diagnosis of periapical cyst was 68.5%, and the accuracy of CBCT in the diagnosis of periapical granuloma was 44.4%. However, CBCT diagnoses are inconsistent with the pathological results for periapical cysts and granulomas (Kappa<0.4). The accuracy of CBCT in the diagnosis of periapical cyst was related to the location of the lesion (P=0.033), residual epithelium (P=0.036), and foam cells (P=0.027) but not to cholesterol cleft, hemorrhage, calcification, acute and chronic inflammation, and the degree of inflammation (P>0.05). Expression of epithelial markers in periapical cysts and odontogenic keratocysts: CK14 and CK19 were positively expressed in most cases, and CD57 was negatively expressed. Expression of markers of cell proliferative activity: Ki-67 positivity in periapical cysts ranged from 1% to 3%, severe infection increased Ki-67 positivity to 15%, and Ki-67 positivity in odontogenic keratocysts ranged from 1% to 3% or 10% to 80%. Conclusion The sensitivity of CBCT in the diagnosis of periapical cysts and periapical granulomas is good, but the specificity is poor. The accuracy of CBCT in the diagnosis of periapical cysts is related to the location of the lesion, residual epithelium, and foam cells but not to cholesterol cleft, hemorrhage, calcification, acute and chronic inflammation, and the degree of inflammation. The number of Ki-67-positive cells in patients with odontogenic keratocysts was higher than that in periapical cysts, and the positive cells were mainly located in the accessory basal cell layer.