The National Trachoma Surveillance and Reporting Unit has reported data for trachoma endemic regions and communities in the Northern Territory, South Australia and Western Australia for 2006 to 2008. Aboriginal children aged 1-9 years were examined using the World Health Organization grading criteria. Screening in the Northern Territory was conducted by the primary health care staff from the Healthy School Age Kids program, the Australian Government Emergency Intervention and Aboriginal Community Controlled Health Services. Forty-three of 92 communities in 6 regions were screened and reported data (2,462 children). In South Australia, the Eye Health and Chronic Disease Specialist Support Program and a team of eye specialists visited 11 of 72 communities in regions serviced by 6 Aboriginal Community Controlled Health Services (365 children). In Western Australia, population health unit and primary health care staff screened and reported data for 67 of 123 communities in 4 regions (1,823 children). Prevalence rates of active trachoma varied between the regions with reported prevalence ranging from 4%-67% in the Northern Territory, 0%-13% in South Australia and 8%-25% in Western Australia. Statistical comparisons must be viewed with caution due to the year-to-year variation in the coverage of children examined and the small numbers. Comparisons of 2006, 2007 and 2008 regional prevalence of active trachoma showed that many communities had no change in prevalence, though there were a few statistically significant increases and decreases (P<0.05). The number of communities screened and the number of children examined has improved but still remains low for some regions. The implementation of the World Health Organization Surgery (for trichiasis), Antibiotics (with azithromycin), Facial cleanliness and Environmental improvement (SAFE) strategy has been variable. Few data continue to be reported for the surgery and environmental improvement components. In general, the availability of the community programs for surgery, antibiotic treatment, and facial cleanliness has improved. Reporting of antibiotic treatment has improved from 2006 to 2008. No significant changes were noted in bacterial resistance reported by pathology services from 2007 to 2008; these rates are comparable to national data collected by the Advisory Group on Antibiotic Resistance in 2005.