Introduction The WHO global initiative on elimination of trachoma by 2020 (GET 2020) recommends mapping of trachoma at district (Local Government Area (LGA)) levels to enable planning and control activities in affected communities worldwide. The aim of the present study was to provide baseline data on trachoma for the LGAs of Sokoto and Kebbi states, Nigeria.

Methods A population-based cross-sectional survey was conducted in 25 LGAs between November 2011 and May 2012. The WHO guidelines for trachoma control and risk factor assessment were used in the planning and conduct of the survey.

Results The prevalence of trachomatous inflammation—follicular in children aged 1–9 years ranged from 0.3% in Sokoto South to 15.6% in Kalgo LGA. The prevalence of trachomatous trichiasis (TT) in adults (>14 years) ranged from 0.03% in three LGAs to 0.6% in Gudu LGA. Logistic regression analysis for the trachoma risk factors after χ² analysis showed only distance from water source as a significant risk factor (OR>1, p<0.5). Clean face, access to latrines and knowledge of trachoma prevention were significantly protective (OR<1, p<0.5) against active disease. The average number of persons in need of TT lid surgery ranged from 0 in 3 LGAs to 397 in Danko-Wasagu LGA. Mass antibiotic distribution is needed in 4 LGAs. The estimated number of households in need of latrines and improved water sources are high, with 1 LGA requiring 34 500 latrines and 20 000 improved water sources.

Conclusions There is a burden of active trachoma of different endemicity levels in all the surveyed LGAs. The burden of trachoma risk factors remains a challenge despite the global effort to decrease the risk factors through the Millennium Development Goals.