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AbstractThis paper examines the link between a mother's autonomy—the freedom and ability to think, express, make decisions and act independently—and the nutritional status of her children. We treat 'autonomy' as a latent variable, and design a novel statistical framework to measure this. This method allows us to separate the direct associations of maternal and family characteristics in our model for nutrition, from their indirect associations that work through maternal autonomy. Using data from India, we explore the sensitivity of our estimates to endogeneity caused by sample selection in the presence of son preference. We find: (i) a one standard deviation (SD) higher autonomy score is associated with a 0.16 SD higher height‐for‐age z‐score (HAZ score); and (ii) a 10% lower prevalence of stunting (HAZ < −2 SD). The latter is equivalent to the prevention of approximately 300,000 children stunting, indicating the important role of maternal autonomy.