Prospective cohort studies of sexually transmitted infections (STIs) are logistically impractical owing to time and expenses. In schools, students are readily available for school-related follow-ups and monitoring. Capitalizing on the logistics that society already commits to ensure regular attendance of adolescents in school, a school-based STI screening in New Orleans made it possible to naturally observe the occurrence of chlamydia and to determine its incidence among 14-19-year-old adolescents. Among participants screened repeatedly, we calculated incidence rates, cumulative incidence, and incidence times. Male (n = 3820) and female (n = 3501) students were observed for 6251 and 5143 person-years, respectively, during which 415 boys and 610 girls acquired chlamydia. Incidence rates per 100 person-years were 6.6 cases for boys and 11.9 cases for girls. In multivariable analysis, the adjusted hazard ratio was 5.34 for boys and 3.68 for girls if the student tested positive for gonorrhea during follow-up, and 2.76 for boys and 1.59 for girls if at first participation the student tested positive for chlamydia, and it increased with age among boys but not among girls. In joinpoint trend analysis, the annual percentage change in the incidence rate was 6.6% for boys (95% CI: -1.2%, 15.1%) and 0.1% for girls (95% CI: -5.3%, 5.7%). Annual cumulative incidence was 5.5% among boys and 8.6% among girls. Median incidence time was 9.7 months for boys and 6.9 months for girls. Our findings can be used to refine assumptions in mathematical modeling and in cost analysis studies of C. trachomatis infection, and provide strong evidence in support of annual chlamydia screening for adolescent boys.