The study of composition and microstructure of welded joints was performed before and after the diffusion annealing at elevated temperatures for different annealing time. The Kirkendall effect in the Ni/Ni3Al diffusion couples was observed by means of different methods, e.g. using light, scanning electron and atomic force microscopies. The study suitably completes and specifies the morphology features of Kirkendall voids at different evolution stages, i.e. at nucleation, growing and coalescence. Kirkendall voids occurred in the region between the Matano and γ/γ´interface planes. The location of the γ/γ´ interface that moved in the direction of Ni3Al phase during the annealing resulted from the Al concentration profile measured by EDAX. The Matano plane location was determined by means of Boltzmann-Matano’s method using concentration profile data. It was observed that the void size was increasing in the direction from the Matano plane to the γ/γ´ interface. The obtained results were completed by surface topography of Kirkendall voids of slightly etched specimens by atomic force microscopy (AFM).