The aim of the present study was to investigate the relation of environmental enteropathy, as measured by the dual sugar absorption test, to linear growth faltering in 2- to 5-year-old Malawian children. Dietary quality, food insecurity, anthropometry, and site-specific sugar testing were measured in 418 children, and anthropometry was reassessed 3 months later. A linear regression model predicting linear growth was created. Better growth was associated with less urinary lactulose excretion, more clean water usage, not sleeping with animals, and no previous history of malnutrition. Eighty-seven percent of children studied demonstrated evidence of environmental enteropathy. In conclusion, abnormal gut integrity is associated with reduced linear growth in a population of rural African preschool-age children.