An important problem in the strength of metal joints of different composition operating at elevated temperatures is the formation of Kirkendall porosity at the interface during operation. The evolving Kirkendall porosity leads to material damage and is particularly dangerous under cyclic loading. The accumulation of the critical value of porosity at the interface can even lead to separation and subsequent failure of the joint. In addition to its practical relevance, the study of Kirkendall porosity is also important from an academic point of view. It contributes to the understanding of the physics of void growth due to diffusion of alloying atoms and vacancies with different mobilities. The mobilities depend on temperature, time and crystallographic orientation of the material. Kirkendall voids have a microscopic size that allows them to be examined typically by optical microscopy (OM) or scanning electron microscopy (SEM). Here, 3D µ-tomography using synchrotron X-rays was applied. Several material joints made of polycrystalline pure Ni and the Ni-based superalloy CMSX-4 were produced by diffusion welding. The CMSX-4 part was varied: Two different crystallographic orientations ([001], [111]) and a non-porous sample produced by hot-isostatic pressing (HIP) were used. Subsequently, to all joints the same annealing temperatures (1150 °C, 1200 °C, 1250 °C, 1300 °C) were applied. Three different annealing times were selected depending on the respective temperature. The morphology, size and distribution of the cavities resulting from the heat treatments were examined by means of 3D µ-tomography. The developing Kirkendall cavities from nucleation and subsequent growth were examined. For example, cubic, pear-shaped, cup-shaped, octahedral, incomplete octahedrons and branched cactus-like structures were found. The less complicated structures were observed at low temperatures and durations close to the diffusion welding interface and, on the other hand, at higher temperatures further away from the interface. The higher the annealing temperature and duration and the closer to the diffusion welding interface, the more complicated the morphology of the Kirkendall voids.