The Northern Territory of Australia has an exceptionally high prevalence of sexually transmitted infections (STIs), particularly in remote areas. In contrast there are few notified cases of HIV at present. This study describes HIV testing rates in both primary care and sexual health clinics in the Top End region. In 2010, medical records were reviewed for a random sample of patients from a sexual health clinic and three remote primary care clinics. Among sexual health clinic patients 51.4% overall, and 59.7% of those with an STI, were tested for HIV. In people diagnosed with an STI in remote primary care clinics 19.1% were tested for HIV. HIV testing rates in the Top End of the Northern Territory do not meet the standard of national and international guidelines, with implications both for the early initiation of therapy and the accuracy of surveillance in a region with very high rates of STIs.