Determination of the three-dimensional (3D) distribution of heterogeneities and structures is of primary concern in the field of materials characterisation and quality control. Heterogeneities may create exploitable property profiles, but they can also degrade reliability and are therefore classified as defects. The quantitative description of heterogeneities is a prerequisite for evaluating their effects and potential for strengthening or degrading a material. Knowledge of the size, shape, location and arrangement of heterogeneities enables the evaluation of the quality of materials and work pieces. Micro-focus X-ray computed tomography (XCT) with flat-panel matrix detectors is the current method of measuring variously absorbing inner or hidden structures without destroying the object. The size and topology of different types of heterogeneities can vary greatly. The different size scales of the heterogeneities and of the affected material volume require appropriate tomographic methods and resolutions. XCT provides statistically significant estimates of volume fractions of heterogeneities in materials depending on the spatial and contrast resolution. The characterisation and quantification of heterogeneities in polymeric materials, light metals, Fe-based materials, metallic foams and metal matrix composites are presented by means of cone beam XCT. Micro-focus and sub-micro-focus X-ray tubes may record intensities related to a minimum volume (voxel size) of (3 μm)3 and (0.4 μm)3, respectively. Spatial resolution also depends on the contrast of the heterogeneity and is usually reliable for features >20 voxels. Suitable evaluation routines are introduced and rules for the detectability and classification of contrast and shape are specified. The architecture of the reinforcement in composite materials is presented and quantified in terms of size distribution, orientation and connectivity. Alignments and the formation of the dendritic structure in cast metals are shown in 3D. A method for differentiation of various heterogeneities which are simultaneously present in one material system is presented. The microstructural features are verified using target metallographic techniques. Thus, important 3D structural information can be achieved to understand their correlation with processing.