In vivo trabecular bone structure measurements have become available recently using high resolution quantitative computed tomography (3D-QCT) or magnetic resonance imaging. In this work different structure extraction and morphometric evaluation techniques are compared, which are of potential use for in vivo assessment of human cancellous bone structure. Given the spatial resolution of actual in vivo examination procedures, best results are obtained by extracting first the skeleton of the structure and applying model independent 3D techniques to calculate trabecular number, then deriving mean trabecular thickness and separation from densitometric bone volume fraction and Tb.N*. Traditional histomorphometric methods based on bone surface and volume ratios and assuming a plate model performed less well.