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.