This prospective case review was performed with the aim to compare and asses the diagnostic values of cone-beam computed tomography (CBCT) and high-resolution computed tomography (HRCT) in the preoperative evaluation of otosclerosis. A total of 43 patients with histologically confirmed stapedial otosclerosis, who underwent unilateral stapedectomies were analyzed. Preoperative temporal bone CBCT and HRCT scans were performed in all cases. Both CBCT and HRCT imaging were characterized by a slice thickness of 0.4–0.625 mm and multiplanar image reconstruction. Histopathologic examination of the removed stapes footplates was performed in all cases. Findings of CBCT and HRCT were categorized according to the modified Marshall’s grading system (fenestral or retrofenestral lesions). Histopathologic results were correlated with multiplanar reconstructed CBCT and HRCT scans, respectively. Negative control groups for CBCT (n = 36) and HRCT (n = 27) examinations consisted of patients, who underwent CBCT imaging due to various dental disorders or HRCT analysis due to idiopathic sudden sensorineural hearing loss. Histologically active foci of otosclerosis (n = 31, 72 %) were identified by both CBCT and HRCT in all cases with a sensitivity of 100 %. However, CBCT could not detect histologically inactive otosclerosis (n = 12, 23 %; sensitivity 0 %). In contrast, HRCT showed inactive otosclerosis with a sensitivity of 59.3 %. According to CBCT results, no retrofenestral lesions were found and the overall sensitivity for hypodense lesions was 61.37 %. In conclusion, CBCT is a robust imaging method in the detection of histologically active fenestral hypodense foci of otosclerosis with high sensitivity and radiologic specificity. In the light of these results, HRCT still remains the basic imaging method in the preoperative diagnosis of otosclerosis, since it has much greater sensitivity and specificity in the detection of retrofenestral hypodense lesions and histologically inactive otosclerotic foci in the oval window niche.