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Cu pumping is the irreversible extrusion of Cu from Cu-filled through-silicon vias (TSVs) exposed to high temperatures during back-end of line (BEOL) processing. The distribution of Cu pumping values over the TSVs of a single wafer has a large intrinsic spread. As potential BEOL reliability issues due to Cu pumping will first occur at the highest pumping TSVs, they can be mitigated if the fundamental cause for this large intrinsic spread is known and under control. This paper describes a clear correlation between Cu pumping and TSV Cu microstructure based on the grain size at the top of 5×50 μm TSV, disregarding twin boundaries. For the mitigation of TSV Cu pumping the ideal microstructure was shown to consist of a single grain spanning the whole TSV cross section, bringing down the highest measured Cu pumping value from 248 nm to 73 nm. This effect was attributed to the absence of rapid diffusion paths and grain boundary sliding ability.