Using the conventional techniques of mineralogy, it has been a challenge to determine mineral identity, crystal orientation and spatial position of micrometer-sized crystals that are embedded in a rock, sediment or soil. Traditionally, the individual grains must be extracted and analyzed separately. Crushing or disintegrating a sample annihilates any possibility for gathering information from the texture of the porous media or the mineral assemblage close to the grains in question. A new method using three-dimensional X-ray diffraction (3DXRD) microscopy can be successfully applied to natural materials. We combined X-ray microtomography (XMT) and 3DXRD to investigate a sample of very fine-grained chalk containing fracture minerals. The XMT technique provides three-dimensional images of the particles and pore structure at very high resolution (350 nm voxel dimension) on samples less than 500 μm in diameter. The minor phases present as crystals in fractures were determined nondestructively with 3DXRD microscopy. The chalk fragment investigated is composed predominantly of randomly oriented nanometric crystals of calcite that produce powder rings where no texture can be observed. Superimposed on this pattern, Bragg diffraction peaks from the other crystalline phases were observed. Individual crystals of barite and pyrite only a few micrometers in diameter are present in the fractures. Magnetite, celestine and siderite, other minerals that might have been expected based on the XMT absorption contrast, were not identified. The crystal shape and in-fracture location, derived from the microtomograms, and the mineral identity, derived from 3DXRD, allowed us to propose that the fractures are original in these tiny drill cuttings; they were not induced by drilling and filled with drilling mud particles, thus allowing reliable estimates to be made of rock porosity and permeability.