Trachoma is the most important infectious cause of blindness worldwide. In two rural populations in Ethiopia, a programme of preventative and treatment measures was initiated in May 2002. A baseline survey was conducted to evaluate the effect of this programme on the prevalence of active trachoma. A total of 1960 children aged 3-9 years, from 915 households in 40 communities, were examined for the presence of active trachoma. Demographic and household information was collected using questionnaires and household amenities and environmental conditions were observed. Overall, 72% of children had active trachoma. Twenty percent of children aged nine years had trachomatous scarring. In children, discharge in the eyes and flies on the eyes were significant indicators of trachoma (odds ratio [OR] = 3.0, 95% CI 1.94-4.55 and OR = 3.4, 95% CI 2.37-4.88, respectively). Frequency of washing children, a clean environment and hygienic disposal of excrement were significant preventative factors for active trachoma. Prevalence of active trachoma varies widely between and within districts. Risk factors comprise a mix of individual characteristics and household factors. This study demonstrates the need for broad target interventions and a flexible approach to the prevention of trachoma in high prevalence endemic rural populations.