Objective To evaluate the reproducibility and accuracy of a new, easy-to-use volumetric assessment of the alveolar cleft. Design Twelve cone-beam computed tomography (CBCT) datasets of patients with a unilateral cleft lip, alveolus, and palate were evaluated by two investigators. Residual alveolar cleft calcified volume one year after surgery was analyzed by using standardized landmarks to determine the borders of the cleft defect and semi-automatically segment the alveolar cleft defect. Results The Dice-coefficient between observers for the segmented preoperative alveolar cleft defect was 0.81. Average percentage of residual alveolar cleft calcified material was 66.7% one year postoperatively. Conclusions This study demonstrates a reliable and practical semi-automatic three-dimensional volumetric assessment method for unilateral clefts using CBCT.