This article uses an innovative rural-urban migrant survey to assess how social disadvantage is associated with children's nutritional status in migrant households. Measures of social disadvantage are based on China's hukou system of household registration (designed to limit domestic migration flows by denying urban public services to migrants with rural registrations) and on son preference (stemming in part from the strict one-child policy). Regression results indicate that a rural hukou status is negatively associated with children's weight-for-age Z-scores, even after controlling for household characteristics, and girl children exhibit poorer nutritional status than boys. Results from a quantile decomposition procedure confirm that left-behind children have lower nutritional scores than children who migrate with their parents, and the gaps are biggest at lower portions of the distribution.