Objective: To compare the radiographic outcome of alveolar cleft bone grafting with expanded mesenchymal stem cells (MSCs) seeded into a resorbable matrix to standard iliac cancellous bone graft. Subjects and methods: Fifteen patients with unilateral alveolar cleft aged 7-12 years old (eight girls and seven boys) were randomly divided, according to grafting technique, into two groups: Group I: Alveolar cleft grafting with expanded autogenous bone marrow stem cells seeded in collagen sponge, platelet rich plasma and nanohydroxyapatite. Group II: Alveolar cleft grafting with cancellous bone harvested from anterior iliac crest. Ideal cleft volume was calculated from cone beam CT with computer aided engineering. Follow up evaluation with cone beam CT. Bone fill was calculated on three and six months postoperatively. Results: The mean ideal cleft volume was 678 mm3 and 726 mm3 in group I and group II respectively with no significant difference. At three months postoperatively, there was a Significantly difference in the mean volume of bone fill (BF) between group I and group II (7% BF, 47% BF respectively). Furthermore, the difference increased significantly at six months to become 10% BF in group I and 60% BF in group II. Conclusion: The hybridized scaffold used in the study for seeding of stem cells that contains collagen sponge, PRP and nanohydroxyapatite still needs improvement in mechanical and biodegradation properties to support bone tissue engineering. Moreover, the radiographic volumetric analysis of cancellous bone graft which is the gold standard revealed suboptimal results that needs further researches to improve the outcome.