BACKGROUND Anogenital warts are a common initial presentation to the Canberra Sexual Health Centre. It is anticipated that the introduction of human papillomavirus vaccination will reduce the incidence of anogenital warts. The present study determines the prevalence of other sexually transmissible infections in patients newly diagnosed with warts who may not have presented for screening without the impetus of a genital lump. METHODS The prevalence of other sexually transmissible infections in new patients presenting to the Canberra Sexual Health Centre diagnosed with anogenital warts was determined from a retrospective clinical audit from 2002 to 2007. RESULTS A total of 1015 new patients were diagnosed with anogenital warts. Of this total cohort, 53 (5.2%) were found to be co-infected with either chlamydia and/or gonorrhoea. Only 13.2% of co-infected patients reported symptoms other than genital lumps. Of co-infected patients 11.3% reported contact with a partner with chlamydia and/or gonorrhoea. Not all patients were screened for other sexually transmissible infections: 762 (75.1%) were screened for chlamydia and 576 (56.7%) were screened for gonorrhoea. Of those tested, 6.8% of men and 6.9% of women were positive for chlamydia highlighting the importance of offering full sexually transmissible infection screening in those newly diagnosed with anogenital warts. Chlamydia was more common in younger patients who reported a higher number of sexual partners. CONCLUSIONS It is anticipated that human papillomavirus vaccination will lead to a decline in anogenital wart incidence as well as other human papillomavirus associated disease. Although one opportunity for testing for other sexually transmissible infections may be lost in this population, the decrease in anogenital warts will leave clinicians with more time to pursue other screening programs. Education and screening campaigns should continue to focus on the asymptomatic nature of the majority of sexually transmissible infections.