ABSTRACT: Despite substantial reductions in recent years in Nepal, stunting prevalence in children younger than 5 years remains high and represents a leading public health concern. To identify factors contributing to the stunting burden, we report multilevel risk factors associated with stunting in 4,853 children aged 6-59 months in a nationally and agroecologically representative random sample from the first year of the Policy and Science for Health, Agriculture, and Nutrition Community Studies, a community-based observational, mixed-panel study. Mixed effects logistic regressions controlling for multilevel clustering in the study design were used to examine the association of individual-, household-, and community-level factors associated with stunting. Stunting prevalence was 38% in our sample. After adjustment for potential confounding variables, maternal factors, including maternal height and education, were generally the strongest individual-level risk factors for stunting, adjusted odds ratio (AOR) = 2.52, 95% CI [1.96, 3.25], short (<145 cm) versus not short mothers; AOR = 2.09, 95% CI [1.48, 2.96], uneducated mothers versus secondary school graduates. Among the household- and community-level factors, household expenditure and community infrastructure (presence of paved roads, markets, or hospitals) were strongly, inversely associated with increased stunting risk, AOR = 1.68, 95% CI [1.27, 2.24], lowest versus highest household expenditure quintile; AOR = 2.38, 95% CI [1.36, 4.14], less developed (lacking paved roads, markets, or hospitals) versus more developed communities. Although most factors associated with stunting are not rapidly modifiable, areas for future research and possible interventions emerged.