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This paper presents a review of the wafer-to-wafer alignment used for 3-D integration. This technology is an important manufacturing technique for advanced microelectronics and microelectromechanical systems, including 3-D integrated circuits, advanced wafer-level packaging, and microfluidics. Commercially available alignment tools provide prebonding wafer-to-wafer misalignment tolerances on the order of 0.25 μm. However, better alignment accuracy is required for increasing demands for higher density of through-strata vias and bonded interstrata vias, whereas issues with wafer-level alignment uniformity and reliability still remain. Three-dimensional processes also affect the alignment accuracy, although the misalignment could be reduced to certain extent by process control. This paper provides a comprehensive review of current research activities over wafer-to-wafer alignment, including alignment methods, accuracy requirements, and possible misalignments and fundamental issues. Current misalignment concerns of the major bonding approaches are discussed with detailed alignment results. The fundamental issues associated with wafer alignment are addressed, such as alignment mechanisms, uniformity, reproducibility, thermal mismatch, and materials. Alternative alignment approaches are discussed, and perspectives for wafer-to-wafer alignment are given.