OBJECTIVE Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) are common sexually transmitted infections that disproportionately affect adolescents. Annual screening for CT for sexually active female adolescents is recommended. In 2006, New York City began conducting CT/GC education, screening, and treatment in public high schools. We examine 3-year programmatic outcomes and the relationship between sexual activity, screening, and CT/GC positivity. METHODS We describe the epidemiology of students who screened and those infected with CT/GC. Univariate, bivariate, and multivariate logistic regression analyses were performed to assess relationships between sex, race/ethnicity, age, sexual activity, and screening status; and the relationship between sexually transmitted infection positivity and sexual activity. RESULTS Between July 2006 and June 2009, we educated 57,418 students and screened 27,353 (47.6%) for CT/GC; 1,736 (6.3%) students were reported to be infected with either organism. Students who screened positive were more likely to be females (8.9%), report black race (8.3%) and be ≥16 years of age (6.6%-9.7%). Screening rates were 70.6% for students who were sexually active, 27.9% for those who had never had sex, and 47.3% for those who did not respond to the sexual activity question; CT/GC positivity was 7.2%, 1.4%, and 6.1%, respectively. CONCLUSIONS Black, older adolescent females were most likely to screen positive for CT/GC in this population. A large proportion of students who did not answer the sexual activity question chose to screen for CT/GC and screened positive. School screening programs should offer screening to all students regardless of reported sexual activity. Programs should target females and older adolescents.