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Abstract Background Stunting remains a considerable public health problem globally, and sex differences in prevalence have been documented. While many risk factors for stunting have been identified, few studies examine how these factors may contribute to sex differences. We test whether: (1) boys and girls are differentially exposed to stunting risk factors, (2) boys and girls respond differently to similar exposures, and (3) these associations are sensitive to the growth measures used. Methods Data comes from 7486 Zambian infants, aged 0–23 months, participating in the SUN (Scaling Up Nutrition) 2.0 Program baseline survey. Surveys and dietary recalls were collected from primary caregivers, and anthropometry was collected for caregivers and children. Stunting was defined as height-for-age z-score (HAZ)