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Distraction osteogenesis (DO) bone regenerate usually suffers from an inferior quality especially with rapid rate. This study was conducted to investigate the effect of mesenchymal stem cells (MSCs) application on different rates of distraction bone quality. Twenty-four goats were divided into group A with standard DO and group B with rapid distraction osteogenesis (RDO) both aided by MSCs. Group C with standard DO and group (D) with RDO were controls. Kruskal-Wallis test and Conover's post hoc analysis was used to evaluate significance (p = 0.05). Histomorphometry showed a strongly significant (SS) increase (p = 0.00036) in trabecular bone (TB) in group A (TB = 174.7 μm, SD = 33.5) and group B (TB = 166.8 μm, SD = 14) compared with group C (TB = 115.4 μm, SD = 19.6) and group D (TB = 86.1 μm, SD = 9.3). There was SS decrease (p = 0.00093) in osteoid percentage (OP) in group A (OP = 13.4%, SD = 2) and group B (OP = 11.5%, SD = 6.5) compared with group C (OP = 27.3, SD = 3.5) and group D (OP = 26.2%, SD = 2.6). Energy dispersive X-ray showed a nonsignificant increase (p = 0.11) in calcification (Ca2+ %) in group A (Ca2+ % = 17.6%, SD = 4.9) and group B (Ca2+ % = 17.6%, SD = 4.3) compared with group C (Ca2+ % = 14.2%, SD = 6.7) and group D (Ca2+ % = 11.5%, SD = 2.4). MSCs application improved microscopic bone quality during standard DO and RDO. However, macroscopic bone quality improvement still needs further investigation.