Trachoma is highly prevalent in remote Indigenous communities in Australia. The National Trachoma Surveillance and Reporting Unit was established in 2006 as a result of a Federal Government initiative to provide comprehensive surveillance data from regional and remote Indigenous communities considered by the jurisdictional population health staff to be 'At Risk' for endemic trachoma, defined as a trachoma prevalence of 5% or more. This report details the findings from the 2009 trachoma screening program together with trends in trachoma prevalence and screening coverage since 2006. Aboriginal children aged 1-9 years resident in At Risk communities were examined for trachoma using the World Health Organization (WHO) simplified trachoma grading criteria. In the Northern Territory, screening was conducted by staff from the Healthy School Age Kids program and the Aboriginal Community Controlled Health Services. In South Australia, screening was conducted by the Eye Health and Chronic Disease Specialist Support Program and a team of visiting ophthalmologists and optometrists. In Western Australia, screening was conducted by staff from State Government population health units and Aboriginal Community Controlled Health Services. In the Northern Territory, 53 of 86 At Risk communities were screened and data were reported for 2283 children. In South Australia, 12 of 72 At Risk communities were screened and data were reported for 149 children. In Western Australia, 68 of 74 At Risk communities were screened and data were reported for 1684 children. The prevalence of active trachoma ranged from 1%-44% in the Northern Territory, 0%-57% in South Australia and 13%-15% in Western Australia. Trend analysis across all three jurisdictions combined found that neither the prevalence of trachoma nor community screening coverage changed significantly between 2006 and 2009. When trend analysis was "done by jurisdiction, there was a significant decrease in trachoma prevalence and a significant increase in community screening coverage only for Western Australia over the same 4 year period. The implementation of the and Environmental improvement (SAFE) strategy has been variable. Surgery referral processes for trichiasis were reported as available in all screened communities in the Northern Territory and South Australia but only in 35% of screened communities in Western Australia. Antibiotics were distributed according to Communicable Diseases Network Australia guidelines in 89% of communities where treatment was indicated. Facial cleanliness programs and resources were reported as poorly implemented in South Australia and Western Australia while minimal data were reported for environmental conditions in all jurisdictions. No significant change was found in bacterial resistance to azithromycin from 2007 to 2009. Significant gaps remain in community screening coverage and in the full implementation of the SAFE strategy. However, the parallel increase in community screening coverage and decrease in trachoma prevalence in Western Australia suggests that the SAFE strategy might have had an effect in reducing trachoma prevalence in that jurisdiction.