PURPOSE: We set out to determine the baseline prevalence of trachoma in 13 Local Government Areas (LGAs) of Borno State, Nigeria. METHODS: A population-based cross-sectional survey was conducted in each of 13 LGAs from 2017 to 2019, with the support of Tropical Data (TD). World Health Organization (WHO)-recommended protocols were used. With a probability-proportional-to-size systematic sampling method, 25 villages were selected per LGA in 2017 and 30 villages per LGA in 2019; in each village, 25 households were enrolled for 2017 surveys, while 30 were enrolled for 2019 surveys. All present, consenting residents aged ≥1 year were examined by TD-certified graders for trachomatous inflammation-follicular (TF) and trachomatous trichiasis (TT) using the WHO simplified grading scheme. Additionally, we collected data on household-level access to water, sanitation and hygiene (WASH) facilities. RESULTS: One LGA (Magumeri) had TF prevalence in 1-9-year-olds ≥10%; two other LGAs (Monguno and Kaga) had TF prevalence between 5.0% and 9.9%. The prevalence of TT unknown to the health system was ≥0.2% in six LGAs. The proportion of households with access to improved water sources ranged from 30% (Kwaya Kusar) to 95% (Monguno); household-level access to improved latrines was lowest in Shani (7%) and highest in Maiduguri (95%). CONCLUSION: Active TT case finding and strengthening of TT surgical services are needed in six LGAs. Mass drug administration (MDA) of antibiotics is needed in three LGAs to reduce the prevalence of active trachoma to below elimination thresholds. The trachoma elimination programme should engage WASH agencies to augment access to improved WASH facilities.