Background. Our knowledge of mandibular growth mostly derives from cephalometric radiography, which has inherent limitations due to the two-dimensional (2D) nature of measurement. Objective. To assess 3D morphological changes occurring during growth in a rabbit mandible. Methods. Serial cone-beam computerised tomographic (CBCT) images were made of two New Zealand white rabbits, at baseline and eight weeks after surgical implantation of 1 mm diameter metallic spheres as fiducial markers. A third animal acted as an unoperated (no implant) control. CBCT images were segmented and registered in 3D (Implant Superimposition and Procrustes Method), and the remodelling pattern described used color maps. Registration accuracy was quantified by the maximal of the mean minimum distances and by the Hausdorff distance. Results. The mean error for image registration was 0.37 mm and never exceeded 1 mm. The implant-based superimposition showed most remodelling occurred at the mandibular ramus, with bone apposition posteriorly and vertical growth at the condyle. Conclusion. We propose a method to quantitatively describe bone remodelling in three dimensions, based on the use of bone implants as fiducial markers and CBCT as imaging modality. The method is feasible and represents a promising approach for experimental studies by comparing baseline growth patterns and testing the effects of growth-modification treatments.