Aflatoxin exposure has been proposed to affect child height-for-age. The following hypothesized associations were tested in Guatemala: (1) aflatoxin (B, B, G, G) exposure and environmental enteric dysfunction (EED) and child height-for-age z-score; and (2) aflatoxin exposures and subsequent symptoms of aflatoxins. Maize consumption data, health data, and samples of maize from households were collected from mothers and their children - under five - in October 2016 (n = 320) and February 2017 (n = 120). Maize samples were tested for aflatoxin levels and maize consumption data were used to compute an aflatoxin exposure level. Results suggest that there was a significant negative correlation between the putative aflatoxin exposure level and child height-for-age z-score (-0.073, p = 0.030), but not for EED. Furthermore, aflatoxin exposure was significantly correlated with aflatoxin symptoms only at the same time point (0.123, p = 0.026). These results support the potential need for engineered solutions to household aflatoxin transmission problems in rural communities of Guatemala.