Trachoma is reported to be hyperendemic in Australia. This study was conducted in a desert area of Central Australia to implement and evaluate the WHO SAFE strategy to control trachoma. The aim of the study was to obtain baseline trachoma prevalence data and to determine whether a single annual visit is adequate for a treatment program targeting households with active cases in a highly mobile population. All registered residents of two Aboriginal communities were eligible for examination. Four visits over the course of 13 months were made to the communities for ocular examinations of residents present at the time of the visit. Examination, diagnosis, and grading of trachoma followed WHO guidelines. The overall examination rate was 75%, refusal rate was <1%, but approximately 50% of community residents were absent during the examination period. Prevalence varied on each visit, but the overall prevalence of active trachoma was 49% over the 13-month period. Children less than 10 years of age had the highest prevalence of active trachoma (79%), over the course of the 13 months, yet the prevalence at any one visit was approximately 60%. Trachomatous scarring was present in 23% of the population. These results suggest that many cases of active trachoma may be missed if a prevalence survey is conducted at only one point in time. Multiple examinations should be conducted to adequately establish prevalence in the population. Antibiotic treatment and health promotion campaigns need to be developed in consideration of local community dynamics.