This study examines the effects of number and sex of siblings on malnutrition of boys and girls under-5 in South Asia. Cross-sectional analyses were conducted on Demographic and Health Surveys data on children under-5 in Bangladesh (N = 7,861), India (N = 46,655) and Nepal (N = 2,475). Data were pooled across countries, and multinomial logistic regression was used to assess the relationship between number and sex of siblings and malnutrition outcomes (wasting, stunting, underweight; based on anthropometric data), adjusting for country and key social and maternal-child health indicators in sex stratified analyses. Number of brothers increased the odds for severe wasting [1 vs. 0 brothers adjusted odds ratio (AOR) = 1.31, 95 % CI = 1.11, 1.55; 2 vs. 0 brothers AOR = 1.36, 95 % CI = 1.07, 1.73] for girls but not boys. Having more male siblings and more female siblings increased the odds of stunting for boys and girls, but effect of 3+ sisters on severe stunting was significantly stronger for girls than boys (girls- 3+ vs. 0 sisters AOR = 2.25, 95 % CI = 1.88, 2.70; boys- 3+ vs. 0 sisters AOR = 1.37, 95 % CI = 1.13, 1.67). For underweight, three or more sisters increased the odds for severe underweight for girls (AOR = 1.27, 95 % CI = 1.04, 1.57) but not boys. Having brothers heightens girl risk for acute malnutrition (wasting), where having multiple sisters increases girl risk for chronic malnutrition (stunting/underweight). Boy malnutrition is less affected by siblings. Findings suggest that issues of son preference/daughter aversion may affect child malnutrition in South Asia.