Micro-computed tomography (µCT) provides quantitative three-dimensional information of bone around titanium implants similar to classical histology. The study, based on an animal model, using cuboid-shaped biofunctionalised Ti6Al4V implants with surrounding bone after 4 weeks, is performed using 3 µCT-systems with X-ray tubes, one synchrotron-radiation-based µCT-system (SRµCT), and classical histology. Although the spatial resolution of the µCTsystems is comparable, only the results of SRµCT agree with results of classical histology. The X-ray tube sources give rise to huge artefacts in the tomograms (interface scattering, beam hardening), which impaired the quantitative analysis of bone up to about 200 µm from the implant surface. Due to the non-destructive character of µCT the specimens can be subsequently examined by classical histologywithout restriction. The quantitative comparison of bone formation uncovers the strong dependence of the detected amount of newly formed bone from the selected slice. Thisimplies the necessity of 3D analysis. SRµCT and classical histology prove that surface modifications of the titanium implant significantly influence the bone formation. Using SRµCT, the preparation artefacts due to cutting and polishing are excluded.