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Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) are the most commonly reported diseases in the USA, with increasing concern regarding cephalosporin-resistant GC strains and growing discussion of routine male screening and analysing extragenital sites. Hospital emergency departments (EDs) may be appropriate screening venues, and our objective was to identify the extent of genital and oropharyngeal CT/GC infection in ED patients.From June 2012 to March 2013, ED patients aged 15–34 were asked to provide a urine sample and oropharyngeal swab for CT/GC analysis and complete a sexual history survey.The 301 female and 192 male participants had a mean age of 25.2 years (SD 4.9); were 65.5% white patients and 33.5% black patients and >85% reported sexual activity in the past year. Tested patient prevalence was 7.7% (any infection/any site; n=38) with no gender differences. Regarding oral infections (n=10), those so infected were more likely to report a friend with a sexually transmitted disease (OR=4.25; CI 1.12 to 16.20), anonymous sex in the past year (OR=5.77; CI 1.58 to 21.15) and belief of some chance of oral infection (OR=5.29; CI 1.31 to 21.28) than those not so infected. Furthermore, four had no corresponding genital infection, and 66.7% (CI 29.1% to 100%) of the oral GC infections were missing concordant genital infection.We find that male and female ED patients have similar likelihood of infection, that 26.3% (CI 12.4% to 40.2%) of those infected have an oral infection and that the majority of oral GC infections would not be identified or treated with urine-based screening. EDs may be important venues to identify those orally infected and provide male screening.