The indolent nature of chlamydia and gonorrhoea, along with the time delay associated with current diagnostic testing, makes definitive diagnosis while in the emergency department impossible. We therefore sought to determine the proportion of patients who receive accurate, presumptive antimicrobial treatment for these infections. A retrospective chart review was performed on all patient encounters that underwent chlamydia and gonorrhoea testing at an urban emergency department during a single month in 2012. Each encounter was reviewed for nucleic acid amplification test results and whether presumptive antibiotics were given during the initial visit. A total of 639 patient encounters were reviewed; 87.2% were female and the mean age was 26.7 years. Chlamydia was present in 11.1%, with women and men having similar infection rates: 10.6% vs. 14.6% (p = 0.277). Gonorrhoea was present in 5.0%, with a lower prevalence among women than men: 3.2% vs. 17.1% (p < 0.001). Women received presumptive treatment less often than men: 37.7% vs. 82.9% (p < 0.001). Presumptive treatment was less accurate in women than men: 7.9% vs. 25.6% (p < 0.001). After combining genders, 10.2% received accurate presumptive treatment; 33.3% were overtreated and 4.4% missed treatment. Presumptive treatment for chlamydia and gonorrhoea was more frequent and more accurate in men than in women. Overall, one-third of patients received unnecessary antibiotics, yet nearly 5% missed treatment. Better methods are needed for identifying patients who need treatment.