This paper describes the purpose and methodology of the Global Trachoma Mapping project (GTMP). The GTMP was set up to complete the baseline trachoma map worldwide by conducting population-based surveys in an estimated 1238 suspected endemic districts of 34 countries. Under GTMP methodology house-to-house cluster random sample surveys are conducted in evaluation units, which generally correspond to “health district” size populations of 100,000-250,000 people. In addition to individual-level demographic and clinical data, household-level water, sanitation and hygiene data are entered into the purpose-built LINKS application on Android smartphones, transmitted to the Cloud, and cleaned, analysed and ministry-of-health-approved via a secure web-based portal. The main outcome measures are the evaluation unit-level prevalence of follicular trachoma in children aged 1-9 years, prevalence of trachomatous trichiasis in adults aged 15?+?years, percentage of households using safe methods for disposal of human faces, and percentage of households with proximate access to water for personal hygiene purposes.