Introduction: For functional and structural restoration of bone deficiencies, various resorbable and nonresorbable alloplastic materials have been introduced, including metals, polymers and ceramics. However, an "optimal" artificial replacement for craniofacial bone has not been found yet and the search for improved reconstruction methods and alternative materials is going on. To assess and compare biocompatibility and osseointegration of these materials, adequate animal test models are indispensable. Methods: In a rabbit cranial defect model, biocompatibility and osseointegration of polymeric and composite bone replacement materials were evaluated at different time points after implantation. Calvaria including implants and surrounding tissue were explanted and embedded in methacrylate resin. The samples were scanned with a nanotom® (phoenix|x-ray) µCT scanner and proceeded for histological examination by sawing-grinding technique. Avizo® Fire (vsg) software was used for visualisation and processing of µCT data. Qualitative and morphometric evaluation of osseointegration and fibrous encapsulation was performed on undecalcified histologic preparations of the explants, and on 3D reconstructions plus virtual slices derived from corresponding 3D µCT datasets. Results: The obtained 3D µCT data enabled a comprehensive qualitative and quantitative assessment of osseointegration and biodegradation of radioopaque composite implants. Prerequisite for visualization and discrimination of materials by µCT is a significant difference of their hounsfield values. Due to this limitation, radiolucent polymeric implant materials and soft tissue could not be distinguished from embedding resin. In contrast, histologic preparations of undecalcified hard tissue and implant materials enabled detailed visualization and examination of all tissues and implant materials. The substantial disadvantage of hard tissue histology was the inevitable loss of information due to small number of slices and large gaps between specimens yielded by this method. Conclusion: To obtain comprehensive and quantifiable information about biodegradation, biocompatibility and osseointegration of alloplastic bone replacement materials, µCT scans as well as histologic evaluation should be performed.