Recent evidence supports the hypothesis that aflatoxin exposure from maize can influence malnutrition rates among children. Therefore, in Guatemala we investigated two questions; which maize sources exposed households to higher risk of aflatoxin exposure symptoms and what the risk factors were for each maize source, pre- and post-maize harvest. Survey data and household maize samples were collected in October 2016 (pre-harvest) and February 2017 (post-harvest) in San Vicente, Guatemala. Structural equation modeling (SEM) and odds ratios were used to assess the data. The results suggested that households which purchased maize from the market had 3.64 higher odds of high levels of aflatoxin. The models identified that good market purchase habits were significant for market-based maize sources while improved post-harvest practices and improved types of maize storage were significant for subsistence-based maize sources. Cumulative results suggest multiple interventions may be effective but are dependent on time of year and source of maize.