Risk factors for the incidence of scarring are needed to inform trachoma control programs in countries hyperendemic for this blinding disease. A cohort of pre-school children with constant, severe trachoma, and an age, sex, and neighborhood matched cohort of children without constant severe trachoma were followed for seven years to determine the incidence of scarring. The incidence of scarring in the children with constant severe trachoma was 29.2% versus 9.6% in the comparison group. In a model adjusting for multiple factors, significant predictors of scarring were increasing age, female, and constant severe trachoma (OR = 4.85, 95% CL = 2.05, 11.40). Infection with C. trachomatis at follow up was also associated with scarring in both groups of children. It is likely that these children have a different host response to infection, and represent a subgroup at high risk for the blinding complications of trachoma. Reducing exposure to infection in the community through antibiotics and changes in hygiene practices is still the most promising control strategy.