A national audit of practice performance against the key performance indicators in the British Association for Sexual Health and HIV (BASHH) and HIV Medical Foundation for AIDS Sexual Health Standards for the Management of Sexually Transmitted Infections (STIs) was conducted in 2011. Approximately 60% and 8% of level 3 and level 2 services, respectively, participated. Excluding partner notification performance, the five lowest areas of performance for level 3 clinics were the STI/HIV risk assessment, care pathways linking care in level 2 clinics to local level 3 services, HIV test offer to patients with concern about STIs, information governance and receipt of chlamydial test results by clinicians within seven working days (the worst area of performance). The five lowest areas of performance for level 2 clinics were participating in audit, having an audit plan for the management of STIs for 2009-2010, the STI/HIV risk assessment, HIV test offer to patients with concern about STIs and information governance. The results are discussed with regard to the importance of adoption of the standards by commissioners of services because of their relevance to other national quality assurance drivers, and the need for development of a national system of STI management quality assurance measurement and reporting.