This study presents a new method for objective assessment of the distraction regenerate using three-dimensional quantitative computer tomography (3D-QCT). The distraction specimens of 16 sheep that underwent bifocal cranial distraction osteogenesis to reconstruct a critical size defect were used to evaluate this method. To analyse the validity of this method the results were compared to conventional quantitative computer tomography (QCT). Squared correlation coefficients ( r 2) according to Sackett showed a high reliability ( r 2>70% for the total DO regenerate, DO Regions 2–4). Method comparison according to Bland-Altman (≤6.25% of measurements out of 95% limits of agreement) showed that three-dimensional computer tomography based bone densitometry is valid for future DO research.