<p>Child malnutrition in India remains among the highest globally, with persistent gender disparities rooted in son preference. Although girls are biologically more resilient, they often receive less food and care in son preferring households. Using nationally representative data from the National Family Health Survey (NFHS-5, 2019–21), this study analysed 112,255 girls aged 0–59&#xa0;months to examine how son preference influences stunting, wasting, and underweight across India’s regions. Son preference was defined as mothers desiring more sons than daughters in their ideal family composition. Generalized linear models with logit links were used to estimate adjusted odds ratios (ORs), controlling for child, maternal, and household characteristics, with analyses conducted nationally and across six regions. Nationally, girls in son preferring households had slightly higher odds of stunting (OR = 1.02; 95% CI: 1.00–1.04), wasting (OR = 1.02; 95% CI: 1.00–1.04), and underweight (OR = 1.02; 95% CI: 1.00–1.04). Regionally, disparities were more pronounced in Central (stunting: OR = 1.04; underweight: OR = 1.06) and Eastern India (stunting: OR = 1.03; underweight: OR = 1.04), while Southern and Northeastern regions showed negligible or reversed associations. Maternal education, higher household wealth, and better maternal nutritional status were protective factors. These findings indicate that son preference contributes to modest but meaningful disadvantages in girls’ nutritional outcomes, particularly in more patriarchal regions. Targeted, gender-transformative strategies within existing nutrition programs are needed, with priority attention to Central and Eastern India while drawing lessons from more gender-equitable regions.</p>