X-ray transmission (XRT) and computed tomography (CT) was used on five samples from the Niaz porphyry Cu–Mo deposit in Iran, representing different alteration zones. Analysis of three-dimensional CT data revealed structural information and groups of elements with low, medium and high attenuation, which were assigned to minerals previously determined by scanning electron microscopy. Thus, the mineralization can be located, and the metal/waste ratio can be estimated, leading to more precise ore body modelling and process parameter determination. CT is useful for selected samples as it is time consuming. XRT can be used as real-time process on conveyor belts.