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This research provides a unified explanation for: (i) the persistence of malnutrition and (ii) the increased prevalence of metabolic disease (diabetes, hypertension, cardiovascular disease) among normal weight individuals with economic development. Our theory is based on an epigenetically determined set point for BMI or bodyweight, which is adapted to conditions of scarcity in the pre-modern economy, but which subsequently fails to adjust to rapid economic change. During the process of development, some individuals thus remain at their low-BMI set point, despite the increase in their consumption, while others who have escaped the nutrition trap (but are not necessarily overweight) are at increased risk of metabolic disease. The theory is validated with microdata from India, Indonesia, and Ghana and can simultaneously explain inter-regional (Asia-Africa) differences in nutritional status and the prevalence of diabetes.