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Background: Pharyngeal and anorectal reservoirs of gonorrhea (GC) and chlamydia (CT) are increasingly recognized among heterosexual women. While a number of studies performed at sexually transmitted disease (STD) clinics have found a high prevalence of extragenital GC/CT infection, such screening is typically not offered during routine primary care visits for women. We sought to define the prevalence of and factors associated with extragenital GC/CT among women in the U.S. Navy., Methods: We recruited servicewomen stationed in San Diego, California, between the ages of 18 and 25 who presented for an annual physical exam between January and September, 2017. Nucleic acid amplification testing was performed on swabs collected at endocervical, oropharyngeal and anorectal sites to assess the presence of GC/CT. An anonymous behavioral questionnaire was also administered to characterize sexual risk. Descriptive statistics were used to compare women with and without a prior history of any sexually transmitted infection (STI) (self-report) along with a current GC/CT diagnosis. This study was approved by the Institutional Review Board of the Uniformed Services University of Health Sciences., Results: Of the 75 patients who were approached, 60 subjects were enrolled in the study, including white 20 (33.3%), black/African American 18 (31.0%), Hispanic/Latina 13 (21.7%) and Asian/Pacific Islander 9 (15.5%) women. Among all the women, six (10.0%) were diagnosed with CT infection, all via endocervical exam. Of these, five (8.3%) had concurrent anorectal infection, including two cases (3.3%) accompanied by pharyngeal infection. Of the subjects, 15 (25.0%) reported anal intercourse in their most recent sexual encounter, most of which was condomless (13/15, 86.7%). A high number of women who reported sex with a casual male partner (19/45, 42.2%) reported rarely or never using condoms; last, 41.7% consuming at least 3 drinks on a typical drinking day, and one-third of the reported drinking more than once per week., Conclusions: We found a high prevalence of anorectal CT infection, although no infections were detected without concurrent endocervical involvement. Nonetheless, the high prevalence of condomless anal intercourse reported by participants argues for further study and ongoing consideration of extragenital screening among high-risk patients. Behavioral interventions are also warranted given the high prevalence of sexual and related risk factors.