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In South Asia, an estimated 38% of preschool-age children have stunted growth. We aimed to assess the effect of WHO-recommended antenatal iron, and folic acid (IFA) supplements on smaller than average birth size and stunting in South Asian children <2 years old. The sample was 96,512 mothers with their most recent birth within two years, from nationally representative surveys between 2005 and 2016 in seven South Asian countries. Primary outcomes were stunting [length-for-age Z-score (LAZ) < -2], severe stunting [length-for-age Z-score (LAZ) < -3], length-for-age Z score, and perceived smaller than average birth size. Exposure was the use of IFA supplements. We conducted analyses with Poisson, linear and logistic multivariate regression adjusted for the cluster survey design, and 14 potential confounders covering the country of the survey, socio-demographic factors, household economic status, maternal characteristics, and duration of respondent recall. The prevalence of stunting was 33%, severe stunting was 14%, and perceived smaller than average birth size was 22%. Use of antenatal IFA was associated with a reduced adjusted risk of being stunted by 8% (aRR 0.92, 95% CI 0.89, 0.95), of being severely stunted by 9% (aRR 0.91, 95% CI 0.86, 0.96) and of being smaller than average birth size by 14% (aRR 0.86, 95% CI 0.80, 0.91). The adjusted mean LAZ was significantly higher in children whose mothers used IFA supplements. Maternal use of IFA in the first four months gestation and consuming 120 or more supplements throughout pregnancy was associated with the largest reduction in risk of child stunting. Antenatal IFA supplementation was associated with a significantly reduced risk of stunting, severe stunting, and smaller than average perceived birth size and improved LAZ in young South Asian children. The early and sustained use of antenatal IFA has the potential to improve child growth outcomes in South Asia and other low-and-middle-income countries with high levels of iron deficiency in pregnancy.