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Background  Human papillomavirus (HPV) vaccination targeting females 12–13 years commenced in Australia in 2007, with catch-up of females 13–26 years until the end of 2009. No analyses of HPV vaccination program impact by either socioeconomic or geographic factors have been reported for Australia.    Methods  Hospital admissions between July 2004-June 2011 involving a diagnosis of genital warts were obtained from a comprehensive national database. We compared sex- and age-specific admission rates in July 2006–June 2007 (pre-vaccination period) and July 2010–June 2011 (post-vaccination period) according to Index of Relative Socio-economic Disadvantage, nationally and stratified by remoteness area relating to the individual’s area of residence, using Poisson/ negative binomial models.    Results  Admission rates per 100,000 population in females aged 10–19 years (predominantly vaccinated at school), reduced from 42.2 to 6.0 (rate reduction 86.7 %; 95 % CI:82.2–90.0 %) in more disadvantaged areas and from 26.8 to 4.0 (85.0 %; 95 % CI:79.7–88.9 %) in less disadvantaged areas. In females aged 20–29 years (predominantly vaccinated in the community), the decreases were from 73.9 to 26.4 (66.0 %; 95 % CI:57.7–72.6 %) and from 61.9 to 23.8 (61.6 %; 95 % CI:52.9–68.7 %) in more and less disadvantaged areas, respectively. The reductions were similar in more vs less disadvantaged areas both inside major cities (88.6 %; 95 % CI: 82.2–92.7 % vs 87.9 %; 95 % CI:82.6–91.6 % in females aged 10–19 years; 64.0 %; 95 % CI:57.0–69.9 % vs 63.8 %; 95 % CI:52.9–72.1 % for females aged 20–29 years) and outside major cities (88.8 %; 95 % CI: 83.7–92.3 % vs 85.8 %; 95 % CI:73.5–92.4 % in females aged 10–19 years; 71.1 %; 95 % CI:58.8–79.7 % vs 67.6 %; 95 % CI:48.2–79.8 % for females aged 20–29 years). Admission rates in males aged 20–29 years also reduced, by 23.0 % (95 % CI:4.8–37.8 %) and 39.4 % (95 % CI:28.9–48.3 %) in more versus less disadvantaged areas respectively.    Conclusions  The relative reduction in genital warts appears similar in young females across different levels of disadvantage, including within and outside major cities, both for females predominantly vaccinated at school and in the community.    Electronic supplementary material  The online version of this article (doi:10.1186/s12879-016-1347-z) contains supplementary material, which is available to authorized users.

bmc infectious diseases

Trends in genital warts by socioeconomic status after the introduction of the national HPV vaccination program in Australia: analysis of national hospital data