In this paper we present a methodology based on 3D synchrotron radiation microtomography to analyze non-destructively 3D bone samples. After a technical presentation of the imaging system and the image analysis techniques, we report results on three-dimensional analysis of vertebral samples from women of different ages. The new capabilities of this technique for the investigation of bone are discussed. They include a high spatial resolution down to the micron level, a high density resolution allowing a local quantification of bone mineralization, phase contrast imaging and advances in 3D image analysis.