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Three-dimensional integrated circuit technology with through-silicon vias offers many advantages, including improved form factor, increased circuit performance, robust heterogenous integration, and reduced costs. Wafer-to-wafer integration supports the highest possible density of through-silicon vias and highest throughput; however, in contrast to die-to-wafer integration, it does not benefit from the ability to bond only tested and diced good die. In wafer-to-wafer integration, wafers are entirely bonded together, which can unintentionally integrate a bad die from one wafer to a good die from another wafer reducing the yield. In this paper, we propose solutions that maximize the yield of wafer-to-wafer 3-D integration, assuming that the individual die can be tested on the wafers before bonding. We exploit some of the available flexibility in the integration process, and propose wafer assignment algorithms that maximize the number of good 3-D ICs. Our algorithms range from scalable, fast heuristics to optimal methods that exactly maximize the yield of wafer-to-wafer 3-D integration. Using realistic defect models and yield simulations, we demonstrate the effectiveness of our methods up to large numbers of wafer stacks. Our results demonstrate that it is possible to significantly improve the yield in comparison to yield-oblivious wafer assignment methods.