Trachoma is the leading infectious cause of blindness in the world. Areas where it is most prevalent also have some of the highest rates of childhood malnutrition. We examined the relationship between both acute and chronic malnutrition and clinical trachoma. We also explored whether malnutrition alters the clinical manifestations of the disease. Children with chronic malnutrition, but not acute malnutrition, were more likely to have clinical trachoma. Stunted children are 1.96 times more likely to have clinical trachoma than nonstunted children (95% CI: 1.12-3.43), even after controlling for age, gender and infection status of other household members. Host factors including malnutrition may play a role in determining disease manifestations.