Nearly 40% of the world's stunted children live in India and the prevalence of undernutrition has been persistently high in recent decades. Given numerous available interventions for reducing undernutrition in children, it is not clear of the relative importance of each within a multifactorial framework. We assess the simultaneous contribution of 15 known risk factors for child chronic undernutrition in India. Data are from the 3rd Indian National Family Health Survey (NFHS-3), a nationally representative cross-sectional survey undertaken in 2005–2006. The study population consisted of children aged 6–59 months [n = 26,842 (stunting/low height-for-age), n = 27,483 (underweight/low weight-for-age)]. Risk factors examined for their association with undernutrition were: vitamin A supplementation, vaccination, use of iodized salt, household air quality, improved sanitary facilities, safe disposal of stools, improved drinking water, prevalence of infectious disease, initiation of breastfeeding, dietary diversity, age at marriage, maternal BMI, height, education, and household wealth. Age/sex-adjusted and multivariable adjusted effect sizes (odds ratios) were calculated for risk factors along with Population Attributable Risks (PAR) and Fractions (PAF) using logistic regression. In the mutually adjusted models, the five most important predictors of childhood stunting/underweight were short maternal stature, mother having no education, households in lowest wealth quintile, poor dietary diversity, and maternal underweight. These five factors had a combined PAR of 67.2% (95% CI: 63.3–70.7) and 69.7% (95% CI: 66.3–72.8) for stunting and underweight, respectively. The remaining factors were associated with a combined PAR of 11.7% (95% CI: 6.0–17.4) and 15.1% (95% CI: 8.9–21.3) for stunting and underweight, respectively. Implementing strategies focused on broader progress on social circumstances and infrastructural domains as well as investments in nutrition specific programs to promote dietary adequacy and diversity are required to ensure a long term trajectory of optimal child growth and development in India.