The use of X-ray micro computed tomography (X-ray micro-CT) for three-dimensional (3D) characterization of multiphase systems continues to increase in metallurgical research. In recent years, a number of technical developments in X-ray sources and X-ray imaging arrays have broadened the utility of micro-CT. Here, the authors review the current state-of-the-art tomographic techniques for both qualitative and quantitative geometallurgical characterization. This review first considers the basic principles of tomography and commonly used tomographic systems. The advantages and disadvantages (shortcomings) of micro-CT are discussed. Software development, including current image reconstruction algorithms, such as traditional weighted back projection and iterative reconstruction algorithms, as well as image segmentation tasks, are then discussed for processing 3D images and conducting quantitative analysis. Based on the development of hardware and software, applications involved in geometallurgy and minerals engineering are then thoroughly discussed. Specifically, applications include the determination of microstructure such as particle size, shape, and damage, as well as porosity and pore network structure of packed particle beds. In this way, the permeability, mineral composition, coal washability, mineral liberation, and exposed grain surface area can be determined.