Objectives Australia introduced a nationwide human papillomavirus (HPV) vaccination programme for women aged 12–26 years in 2007 and has implemented various chlamydia control strategies over the last 10 years. We compared reported diagnoses of warts and chlamydia in two national population-based samples surveyed 10 years apart.

Methods An Australia-wide survey of women aged 18–39 years was conducted by random-digit dialling mobile phone numbers in 2011. The proportion of women self-reporting genital warts and chlamydia was compared with that in equivalent-aged women interviewed in another national telephone survey conducted 10 years earlier using logistic regression adjusting for age, and other factors.

Results 2394 women were included in the 2011 survey. 88 (3.7%) reported a genital warts diagnosis, and 127 (5.3%) had at least one chlamydia diagnosis. For women with warts and chlamydia, the majority were seen in general practice (63.3% and 70.0%, respectively). Comparing women surveyed in 2011 to 4874 women surveyed in 2001, among women eligible for free HPV vaccine through the national programme (women aged 18–30 years), there was a 41% decrease in warts (adjusted OR 0.59, 95% CI 0.39 to 0.89) but among ineligible women (31–39 years) there was a 64% increase (aOR 1.64, 95% CI 1.05 to 2.54). Over the same period chlamydia diagnoses increased by 97% (aOR 1.97, 95% CI 1.15 to 3.37) in women aged 18–24 years.

Conclusions Our results add to evidence from clinic-based studies showing a significant reduction in genital warts among HPV vaccine-eligible women in the general community and increases in the proportion of Australian women diagnosed with chlamydia.