Repeated micro-CT scanning of a number of iliac crest biopsies enabled us to quantitate the variation in CT image gray-scale and spatial geometry due to variables such as specimen orientation, projection magnification, voxel size and slight differences in x-ray photon energy in each of the different scans. Using the micro-CT scanner on beamline X2B at the Brookhaven National Laboratory's National Synchrotron Light Source, we rescanned several iliac crest bone biopsy specimens, and a test phantom made of calcium hydroxyapatite, at repeated scanning sessions and evaluated the reproducibility of the spatial geometry and gray-scale characteristics of the specimens. This scanner consists of a Bragg diffraction source of monochromatic x-rays, a computer controlled high precision specimen rotation and translation stage assembly, and a fluorescent crystal and CCD array system for imaging the specimen at each of the angles of view around its axis of rotation during the scanning sequence. The 3-D micro-CT images consisted of up to 1024×24002, 4 μm, cubic voxels, each with 16-bit gray-scale. We also reconstructed the images at 16, 32 and 48 μm voxel resolution. Partial volume effects at the surface of the bone were diminished by 'eroding' the surface voxels in the 4 μm images, but significantly changed the outcome at greater voxel size. Reproducibility of the mineral content of bone, at mean bone opacity value, was ± 28.8 mg/cm3, i.e., 2.56%, in a 4 μm cubic voxel at the 95% confidence level.