Alignment of a first wafer bonded to a second wafer can be determined using electrical wafer alignment methods. A wafer stack can be formed by overlaying a second wafer over a first wafer such that second metal bonding pads of the second wafer contact first metal bonding pads of the first wafer. A leakage current or a capacitance measurement step is performed between first alignment diagnostic structures in the first wafer and second alignment diagnostic structures in the second wafer for multiple mating pairs of first semiconductor dies in the first wafer and second semiconductor dies in the second wafer to determine the alignment.