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This study examines a catastrophic earthquake in 1923 to analyse the long-term effects of a natural disaster on children’s health. The findings show that foetal exposure to Japan’s Great Kantō Earthquake had stunting effects on girls in the devastated area. Disaster relief spending helped remediate stunting among boys by late primary school age, whereas it did not ameliorate girls’ stunting, which suggests a prenatal selection mechanism and compensating investment after birth. While maternal mental stress due to the fear of vibrations and anticipation of future aftershocks played a role in the adverse health effects, maternal nutritional stress via physical disruption also enhanced those effects.