This methodical study presents a novel approach to evaluate the validity of two-dimensional histomorphometric measurements of a bone biopsy specimen after sinus floor elevation by means of high contrast, high resolution, three-dimensional and non-destructive synchrotron micro-tomography (SCT). The aim of this methodical description is to demonstrate the potential of this new approach for the evaluation of bone biopsy samples.Unilateral sinus grafting was carried out exemplarily in two patients using a combination of β-tricalcium phosphate (β-TCP) and autogenous bone chips. For the first patient a β-TCP with 35% porosity and in the second with 60% porosity was used. At implant placement, 6 months after sinus grafting, a cylindrical specimen was biopsied from the augmented area. Subsequent to the histological embedding in resin the specimens were imaged using a SCT facility resulting in three-dimensional (3-D) images with approximately 4 μm spatial resolution (1.5 μm pixel size) for each patient's specimen. Subsequent to the SCT acquisition, tissue sections were prepared for histomorphometric analysis.Bone area fractions determined by two-dimensional (2-D) quantitative histomorphometry and by analysis of the corresponding 2-D slice from the SCT volume data were similar. For the first biopsy specimen (β-TCP with 35% porosity), the bone area fractions were 53.3% and 54.9% as derived by histomorphometry and by analyzing a SCT slice, respectively. For the second biopsy specimen (β-TCP with 60% porosity) the bone area fractions were 38.8% and 39% respectively. Although the agreement between the 2-D methods was excellent, the area fractions were somewhat higher than the volume fractions computed by 3-D image analysis on the entire SCT volume data set. The volume fractions were 48.8% (first biopsy specimen) and 36.3% (second biopsy specimen).Although the agreement between the 2-D methods is excellent in terms of computing the area fractions, the structural 3-D insight which can be derived from classical 2-D methods, including histomorphometric analysis is considerably limited. This fact is emphasized by the discrepancy between the measured areas and volume fractions.