Background: This study aimed to examine trends in chlamydia and gonorrhoea testing and positivity in Aboriginal and non-Aboriginal women of reproductive age. Methods: A cohort of 318002 women, born between 1974 and 1995, residing in Western Australia (WA) was determined from birth registrations and the 2014 electoral roll. This cohort was then probabilistically linked to all records of chlamydia and gonorrhoea nucleic acid amplification tests conducted by two large WA pathology laboratories between 1 January 2001 and 31 December 2013. Trends in chlamydia and gonorrhoea testing and positivity were investigated over time and stratified by Aboriginality and age group. Results: The proportion of women tested annually for chlamydia increased significantly between 2001 and 2013 from 24.5% to 36.6% in Aboriginal and 4.0% to 8.5% in non-Aboriginal women (both P-values <0.001). Concurrent testing was high (>80%) and so patterns of gonorrhoea testing were similar. Chlamydia and gonorrhoea positivity were substantially higher in Aboriginal compared with non-Aboriginal women; age-, region-A nd year-adjusted incidence rate ratios were 1.52 (95% confidence interval (CI) 1.50-1.69, P<0.001) and 11.80 (95% CI 10.77-12.91, P<0.001) respectively. Chlamydia positivity increased significantly in non-Aboriginal women aged 15-19 peaking in 2011 at 13.3% (95% CI 12.5-14.2%); trends were less consistent among 15-19-year-old Aboriginal women but positivity also peaked in 2011 at 18.5% (95% CI 16.9-20.2%). Gonorrhoea positivity was 9.7% (95% CI 9.3-10.1%), 6.7% (95% CI 6.4-7.0%), 4.7% (4.4-5.0%), and 3.1% (2.8-3.4%) among Aboriginal women aged respectively 15-19, 20-24, 25-29 and ≥30 years, compared with <1% in all age groups in non-Aboriginal women. Over time, gonorrhoea positivity declined in all age groups among Aboriginal and non-Aboriginal women. Conclusion: Between 2001 and 2013 in WA chlamydia and gonorrhoea positivity remained highest in young Aboriginal women despite chlamydia positivity increasing among young non-Aboriginal women. More effective prevention strategies, particularly for young Aboriginal women, are needed to address these disparities.