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The relevance of screening of oropharynx and anorectum in addition to endocervical tests for detection of Chlamydia trachomatis and Neisseria gonorrhoeae infection is unclear in women, while there is a documented benefit of this approach in men who have sex with men.Female visitors to the sexually transmitted disease (STD) clinic were asked about their sexual practice as a part of the routine electronic patient file. In addition to tests for endocervical infection, swabs were taken from the oropharynx and anorectum to test for C. trachomatis and N. gonorrhoeae based on the history of sexual contact. Routinely, all electronic patient files are anonymously included in a database for surveillance purposes. In this observational study, we analyzed all consultations in the database over an 18 months period.A total of 4299 consultations were registered; 10% of women had endocervical chlamydia and 1.1% had gonorrhea. The detection rates for C. trachomatis and N. gonorrhoeae from oropharyngeal samples were 1.9% and 0.8%, and from anorectal samples 8.7% and 1.7%, respectively. Except for 2 cases of pharyngeal gonorrhea, all oropharyngeal and anorectal infections were asymptomatic. Inclusion of oropharyngeal and anorectal tests in the screening protocol was associated with a percentage increase in prevalence of chlamydia by 9.5% and gonorrhea by 31%, relative to tests for endocervical tests alone. The percentage increase in prevalence was higher than that for the symptom-based approach (3.7% and 10.4%, respectively).Inclusion of oropharyngeal and anorectal tests in the STD screening protocol increases the prevalence of chlamydia and gonorrhea in women. Screening of anatomical sites based on sexual history is preferred over a symptom-based protocol.