OBJECTIVES: To determine by systematic review the prevalence of genital chlamydial infection in Australia between 1997 and 2004. METHODS: Electronic literature databases, reference lists, and conference proceedings were searched and health agencies and jurisdictions were contacted for published and unpublished reports. Studies were eligible if they offered a diagnostic nucleic acid amplification test to consecutive individuals presenting during the study period. As a summary measure of the available data, mean prevalence rates, weighted by sample size and irrespective of participant age, were calculated for the population sub-groups. RESULTS: 40 studies of 50 populations and 40,587 individuals met the inclusion criteria, but only one of these was population-based. The use of non-systematic methodologies prevented an assessment of time trends and a statistical comparison of population sub-groups. The mean overall prevalence of genital chlamydial infection was 4.6% (95% CI 4.4-4.8%), reflecting over-sampling of high-risk groups. The mean community-based rates were 7.5% (95% CI 6.4-8.6%) and 8.7% (95% CI 7.9-9.7%) for Indigenous men and women, and 1.5% (95% CI 1.1-1.9%) and 1.4% (95% CI 0.9-2.0%) for non-Indigenous men and women. The overall mean estimates for other groups were 3.3% (95% CI 3.0-3.7%) for female attendees of sexual health and related clinics, 5.6% (95% CI 4.9-6.4%) for adolescents and young adults, 3.3% (95% CI 2.8-3.9%) for sex workers, and 1.6% (95% CI 1.2-2.0%) for urethral infection in men who have sex with men. Clinic-based estimates were generally, although not consistently, higher than community-based estimates. There is no serial population-based data for sexually active young men and women, but the available age-specific rates suggest under-ascertainment by the routine surveillance systems. CONCLUSIONS: The prevalence of genital chlamydial infection in Indigenous Australians and young adults is unacceptably high and quality epidemiological studies are urgently required to supplement the routinely collected national notification data.