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The objective of this study was to examine the proportion of missed infections and correlates of pharyngeal gonorrhea among young people attending public sexually transmitted disease (STD) clinics.We conducted a case-control study of 245 young men and women between April 2012 and May 2014. Participants were eligible for inclusion if they (1) were 15 to 29 years of age, (2) reported giving oral sex to a partner of the opposite sex in the past 90 days, and (3) attended 1 of 12 public STD clinics in Los Angeles County. Computer-assisted self-interviews were used to collect information on sexual behaviors and tests were conducted for pharyngeal and urogenital gonorrhea.Most participants were younger than 25 years (69%) and more than half were female (56%). We identified a total of 64 cases (27%) of gonorrhea, of which 29 (45%) were a urogenital only infection, 18 (28%) were a pharyngeal only, and 17 (27%) were dually infected at both sites. Pharyngeal testing increased case finding by 39% from 46 to 64 cases. After adjusting for age, sex, and number of sex partners, those who reported consistent pharyngeal exposure to ejaculate/vaginal fluids were 3 times as likely to have pharyngeal gonorrhea as compared with those without this exposure (adjusted odds ratio, 3.1; 95% confidence interval, 1.3–7.5).A large proportion of gonorrhea cases among young people would be missed in the absence of pharyngeal testing. These results have implications for those who provide medical care to clients at STD clinics and highlight the need for pharyngeal screening recommendations and counseling messages related to strategies to reduce exposure to infected fluids.