Background In Australia, testing and treatment for HIV and other sexually transmissible infections (STIs) is usually managed in general practice, while publicly funded sexual health clinics (PFSHC) attract people at higher risk for infection. The proportion of HIV and STI diagnoses in New South Wales (NSW) occurring in PFSHC stratified by priority population was investigated. From 2010 to 2014, NSW notification frequencies for chlamydia, gonorrhoea, infectious syphilis, and HIV were compared with the number of diagnoses in PFSHC. The annual proportion of diagnoses at PFSHC was calculated and Wilcoxon rank-sum tests assessed trends. Diagnoses from PFSHC were also organised by priority population, including gay and bisexual men (GBM), people living with HIV, Aboriginal and Torres Strait Islander people, people who use injecting drugs, sex workers and young people. The annual proportion of HIV and STIs diagnosed at PFSHC increased (all P<0.001): chlamydia from 12% to 15%, gonorrhoea 23% to 38%, infectious syphilis 21% to 40% and HIV 22% to 30%. Overall, the majority of all infections diagnosed at PFSHC were among GBM, with the proportional distribution of chlamydia increasing from 32% to 46% among GBM (P<0.001) and decreasing among young people (50% to 40%; P<0.001). There were no other significant changes by population or infection at PFSHC. Increasing proportions of STI and HIV are being diagnosed at NSW PFSHC, mostly among GBM. PFSHC reorientation to priority populations continues to make a large and increasing contribution to STI and HIV control efforts in NSW.