Three-dimensional microstructure reconstructions of Ni yttria-stabilized zirconia (Ni/YSZ) anodes are presented, all of which are based on focused ion beam tomography data. The reconstruction procedure, starting from a series of 2D scanning electron micrographs, is investigated step by step and potential sources of error are identified. The distinction between Ni phase, YSZ phase and pore phase is solved by an advanced algorithm, which belongs to the region-growing image segmentation methods. This improves the accuracy of automated grayscale segmentation especially for images with low contrast, which is characteristic of both solid phases in Ni/YSZ anodes. Critical microstructure parameters like material fractions, surface areas, particle size and distribution of Ni, YSZ, and pore phase, as well as phase connectivity and triple-phase boundary density, are evaluated and discussed. In this contribution, two types of high-performance Ni/YSZ anodes differing in thickness of both the anode functional layer and the anode substrate are reconstructed and compared to each other. For the first time, the anode functional layer adjacent to the thin film electrolyte is separately quantified. The presented methods are qualified to quantitatively compare different anode microstructures and relate the result to their electrochemical performance. (C) 2013 Elsevier B.V. All rights reserved.