OBJECTIVES: To estimate the costs and benefits of patient pathways incorporating a point of care nucleic acid amplification test (POC NAAT) for chlamydia and gonorrhoea in genito-urinary medicine (GUM) clinics in the UK compared with standard off-site laboratory testing. METHODS: We simulated 1.2 million men and women GUM clinic attendees based on GUMCAD reports from the UK (2011). A Markov model with Monte Carlo simulation in Microsoft Excel was developed to compare existing standard pathways of testing and treatment for chlamydia and gonorrhoea with a POC NAAT. We conducted sensitivity analyses to evaluate the robustness of the model findings. The primary outcome was the incremental cost-effectiveness ratio (ICER = £/QALY). Secondary outcomes included the number of inappropriate treatments, complications and transmissions averted and change in time from test to treatment. RESULTS: The total cost of using the POCT in our cohort was £103.3 million compared with £113.9 million for standard care.  The ICER was -£4,182/QALY, making the new pathways cost saving. Nearly 100,000 inappropriate treatments might be avoided by using a POC NAAT. Patients receive diagnosis and treatment on the same day as testing, which may also prevent 162 cases of pelvic inflammatory disease and 17,561 transmissions. CONCLUSIONS: Replacing standard laboratory tests for chlamydia and gonorrhoea with a POCT could be cost saving and patients would benefit from more accurate diagnosis and less unnecessary treatment. Overtreatment currently accounts for about a tenth of the reported treatments for chlamydia and gonorrhoea and POC NAATs would effectively eliminate the need for presumptive treatment.