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Human migration attributable to climate events has recently received significant attention from the academic and policy communities 1, 2. Quantitative evidence on the relationship between individual, permanent migration and natural disasters is limited 3, 4, 5, 6, 7, 8, 9. A 21-year longitudinal survey conducted in rural Pakistan (1991–2012) provides a unique opportunity to understand the relationship between weather and long-term migration. We link individual-level information from this survey to satellite-derived measures of climate variability and control for potential confounders using a multivariate approach. We find that flooding—a climate shock associated with large relief efforts—has modest to insignificant impacts on migration. Heat stress, however—which has attracted relatively little relief—consistently increases the long-term migration of men, driven by a negative effect on farm and non-farm income …