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Harvest of the autogenous iliac crest bone graft for an alveolar cleft defect (the gold standard) may cause short- and long-term pain and sensory disturbances. To determine if a tissue engineering technique with similar bone healing results offered decreased morbidity, we compared techniques for postoperative donor site pain. Traditional iliac crest bone graft had more donor site complications compared with both tissue engineering and minimally invasive iliac crest bone graft. With donor site pain, traditional had the most patients with pain and tissue engineering had the least patients with pain at all time points. The mean pain score, including both intensity and pain frequency, was greatest at all time points in traditional and least at all time points in tissue engineering. Closure of alveolar cleft defects with a resorbable collagen sponge and bone marrow stem cells resulted in reduced donor site morbidity and decreased donor site pain intensity and frequency.