Severe bone loss in weight bearing bones is one of the main causes for morbidity in trauma victims. The use of guided bone regeneration in the treatment of such large defects has not yet been studied extensively. The aim of this study was to establish an accurate evaluation system, which will enable quantifying the compatibility of membranes to provide bone regeneration in a large middiaphyseal bone defect. In our longitudinal study on 16 rabbits we examined the new bone formation obtained in the vicinity of critical segmental defects (2.5 times the diameter of the bone) covered with tubular ethyl cellulose membranes. The contralateral limbs with the same bone defect served as the control group which was not treated by membranes. The healing process was followed up for eight weeks. Bone analysis of the implanted and non-implanted bone defects and adjacent tissues was performed in order to evaluate the total area and the density of the regenerated new bone at the gap area. Computerized X-ray study showed newly formed bone as early as 14 days after membrane implantation within and around the radial defect compared with a typical creation of non-union in the contra-lateral non-implanted defects. The bone formation across the gap progressed until reconstruction of the defect occurred after 6–8 weeks. A slowdown in new bone formation was evident after 6 weeks according to the measurements of area size and density of the formed bone. A parallel longitudinal histomorphological assessment of the process in the treated and non-treated bone defects was conducted. A characteristic process of osteogenic activity and new bone formation takes place inside the confined space and within the tissues around it. A typical modeling process with lytic changes in the different osteogenic fronts takes place from the second week post-implantation. These histological findings, corresponding with the radiological assessment, were summarized according to a scoring system which was constructed by the authors. The scoring was related to eight different zones which were defined within and around the osteotomy site. This rabbit model clarifies the mechanism and provides quantification of guided bone regeneration. It can serve as a means to study the accelerated bone formation using different membranes in large segmental weight bearing bone defects.