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Quantification of the bone healing processes by X-ray-based methods becomes inaccurate in the presence of radiopaque synthetic materials. In this study, single photon emission computed tomography (SPECT) and positron emission tomography (PET) were compared as alternatives to follow in vivo bone healing in a rat calvarial defect model. SPECT/computed tomography (CT) following administration of 99m technetium-labelled hydroxymethylene diphosphonate (99m Tc-HDP) and PET/CT data with 18 F-fluoride were acquired up to 10 weeks after surgery. New bone formation was then confirmed by histology. Computed tomography scans allowed visualization of untreated bone defect healing; however, no information was gathered in presence of the ceramic. Positron emission tomography provided superior data compared with SPECT. The 18 F-fluoride uptake increased significantly up to 4 weeks after surgery, declining thereafter until the last time-point. In vivo performances of porous versus dense ceramic scaffolds were also evaluated by PET, with a significantly higher uptake registered within the porous scaffolds. In conclusion, PET is a valuable tool for qualitative/quantitative follow-up of bone healing around radiopaque bone substitutes in vivo. Copyright © 2014 John Wiley & Sons, Ltd.