BACKGROUND: To determine where interventions are needed to eliminate trachoma as a public health problem, prevalence data are needed. We aimed to generate baseline population-based data on trachoma prevalence in suspected-endemic areas of Afghanistan. METHODS: Cross-sectional population-based prevalence surveys designed according to World Health Organization (WHO) recommendations were conducted in 35 evaluation units (EUs) covering 72 districts. In selected households, all resident individuals aged ≥1 year were examined for trachomatous inflammation-follicular (TF) and trachomatous trichiasis (TT) according to the WHO simplified trachoma grading system. Water, sanitation and hygiene access was assessed in households of survey participants. RESULTS: 104,104 people aged ≥1 year were examined, including 43,774 children aged 1-9 years and 46,439 people aged ≥15 years. The age-adjusted prevalence of TF in 1-9-year-olds was ≥5% in 3 EUs, with the highest EU TF prevalence being 7.8%. The age- and gender-adjusted prevalence of TT unknown to the health system in ≥15-year-olds was <0.2% in all EUs. The majority of households had access to an improved water source within 30 minutes of the house. However, only a minority of households had an improved latrine and/or a handwash station. CONCLUSIONS: Trachoma is not a public health problem in the majority of EUs surveyed. However, antibiotic mass drug administration, promotion of facial cleanliness and environmental improvement (the A, F and E components of the SAFE strategy) are needed for trachoma elimination purposes in three of the EUs surveyed in Afghanistan.