The aim of this study is to evaluate the use of the bone marrow aspirate in a resorbable matrix for repair of alveolar cleft defects together with evaluating its morbidity at the iliac crest donor site. The study was carried on twelve patients with alveolar cleft, comparing the post opertative results of autogenous iliac crest bone graft and bone marrow aspirate on a collagen carrier as an alternative grafting material with minimum morbidity.The twelve patients were divided into two equal groups: group A were grafted with autogenous iliac crest as a standardized control grafting material, while group B were grafted with the bone marrow aspirate on a collagen carrier. Thorough preoperative assessment of all the patients was carried out including: patient history, clinical and radiographic examination.Based on our clinical results, we believe that bone marrow aspirate with a resorbable collagen carrier is a promising grafting material for reconstruction of the alveolar cleft defects in young patients, with the best results regarding the donor site morbidity allowing patients returning to normal function within an acceptable time frame and with an aesthetically acceptable donor site scar.Our radiographic evaluation showed that the amount of the formed bone in the aspirate group was not great enough, but the lack of the donor site morbidity, decrease in the time of the hospitalization and good soft tissue healing may be good criteria for future comprehensive research in Mesenchymal stem cells based bone engineering.The future of alveolar cleft grafting will likely involve tissue engineering.Nevertheless, the controversies regarding the correct timing of treatment and the most appropriate donor sites will continue as will further research into less morbid therapies.In conclusion, this study supports the view that the iliac crest can still be considered as the gold standard for bone regeneration, but we recommend the use of the bone marrow aspirate with the collagen carrier as an acceptable alternative grafting material in the alveolar cleft patients only in young patients (in the mixed dentition stage) with small sized defects, especially in the case of limited autograft availability or donor site morbidity. Finally, we could assure that we have entered a new era in the regeneration of oro-facial bone, where molecular enhancement by osteoinductive materials and stem-cell-based therapies can be used to improve the clinical outcomes and ultimately offer long term benefits to patients.