Background Stunting is an indicator of poor linear growth in children and is an important public health problem in many countries. Both nutritional deficits and toxic exposures can contribute to lower height-forage Z-score (HAZ) and stunting (HAZ <-2). Objectives In a community-based cross-sectional sample of 97 healthy children ages 6-59 months in Kampala, Uganda, we examined whether exposure to Pb, As, Cd, Se, or Zn were associated with HAZ individually or as a mixture. Methods Blood samples were analyzed for a mixture of metals, which represent both toxins and essential nutrients. The association between HAZ and metal exposure was tested using multivariable linear regression and Weighted Quantile Sum (WQS) regression, which uses mixtures of correlated exposures as a predictor. Results There were 22 stunted children in the sample, mean HAZ was-0.74 (SD = 1.84). Linear regression showed that Pb (β =-0.80, p = 0.021) and Se (β = 1.92, p = 0.005) were significantly associated with HAZ. The WQS models separated toxic elements with a presumed negative effect on HAZ (Pb, As, Cd) from essential nutrients with presumed positive effect on HAZ (Se and Zn). The toxic mixture was significantly associated with lower HAZ (β =-0.47, p = 0.03), with 62% of the effect from Pb. The nutrient WQS index did not reach statistical significance (β =-0.47, p = 0.16).