Background: Autogenous bone graft is the gold standard for repair of bone defects. However, osteoprogenitor stem cells are suggested as an alternative treatment. Aims: To quantitatively compare bone formation in autogenous bone graft and tissue-engineered graft using digital radiography densitometry software in canine alveolar cleft model. Setting and Design: This experimental study on animal models was conducted in Isfahan University of Medical Sciences. Methods: Mesenchymal stem cells (MSCs) were obtained from subcutaneous adipose tissue of 4 dogs. Undifferentiated cells were incubated with a hydroxyapatite/beta-tricalcium phosphate scaffold in an osteogenic medium for 21 days. A maxillary defect simulating human alveolar cleft was created from the alveolar crest to nasal floor with 15 mm width bilaterally. Two months later, the defect was filled with autogenous bone graft harvested from tibia on one side and tissue-engineered graft from MSCs on the other side. Digital radiography was performed on days 15, 30, 45, 60, 75, and 90 after grafting. Radiographic density was calculated by the mean numeric value of pixels of the desired area ranging from 0 (darkest) to 255 (lightest) by associated software. Statistical Analysis Used: The data were analyzed by Statistical Package for the Social Sciences using descriptive statistics and two-way repeated-measure analysis of variance test (α = 0.05). Results: Mean density measured for autogenous bone graft group was 110.72, 82.70, 75.76, 93.57, 100.22, and 100.32 in days 15, 30, 45, 60, 75, 90, respectively and 120.7, 87.62, 83.72, 92.02, 92.30, and 93.77 in stem cell group. Although the time lapse was a significant factor in two groups (P = 0.01), the results indicated that the difference between two groups was not statistically significant (P = 0.942). Conclusion: Tissue-engineering can be used as an alternative method in reconstruction of bony defects with predictable clinical outcomes.