Background The bone graft for the alveolar cleft has been accepted as one of the essential treatments for cleft lip patients. Precise preoperative measurement of the architecture and size of the bone defect in alveolar cleft has been considered helpful for increasing the success rate of bone grafting because those features may vary with the cleft type. Recently, some studies have reported on the usefulness of three-dimensional (3D) computed tomography (CT) assessment of alveolar bone defect; however, no study on the possible implication of the cleft type on the difference between the presumed and actual value has been conducted yet. We aimed to evaluate the clinical predictability of such measurement using 3D CT assessment according to the cleft type. Methods The study consisted of 47 pediatric patients. The subjects were divided according to the cleft type. CT was performed before the graft operation and assessed using image analysis software. The statistical significance of the difference between the preoperative estimation and intraoperative measurement was analyzed. Results The difference between the preoperative and intraoperative values were $-0.1{pm}0.3cm^3$ (P=0.084). There was no significant intergroup difference, but the groups with a cleft palate showed a significant difference of $-0.2{pm}0.3cm^3$ (P<0.05). Conclusions Assessment of the alveolar cleft volume using 3D CT scan data and image analysis software can help in selecting the optimal graft procedure and extracting the correct volume of cancellous bone for grafting. Considering the cleft type, it would be helpful to extract an additional volume of $0.2cm^3$ in the presence of a cleft palate.