Secondary alveolar cleft repair using autologous bone graft is currently the gold standard in treating residual alveolar clefts. Despite its effectiveness, this technique is still burdened by several withdrawals, mostly related to donor site morbidity. To decrease disadvantages for patients, numerous attempts in the literature regarding bone substitutes have been described. The aim of this study is to compare the viability of bovine-based replacement bone material with respect of autologous bone graft in alveolar cleft reconstruction, through 3-dimensional alveolar cleft segmentation and bone density evaluation from preoperative and postoperative cone-beam computed tomography. A retrospective cohort study of 10 patients who underwent surgical procedure for alveolar cleft grafting at Sant'Orsola Malpighi University Hospital of Bologna from December 2012 to December 2016 was undertaken. Five patients received autologous bone graft and 5 a bovine bone substitute graft. Preoperative and immediate postoperative orthopanoramic x-rays were recorded. Cone-beam computed tomography scans have recorded both pre and postoperatively. Volumetric evaluation on 3-dimensional cone-beam computed tomography images was performed. Alveolar clefts repaired using substitute bovine bone/biological membrane scaffold had a mean fill of 69.00% of total cleft volume, while this figure was of 67.07% with autologous bone grafting. The immediate postoperative course and subsequent discharge were uneventful for both groups, with a difference in timing. The cost of substitute bovine bone was offset by cost savings associated with a reduction in operative and postoperative and hospitalization time. Bone substitutes showed to be a promising solution in alveolar cleft grafting.