Genital Chlamydia trachomatis infection is common and treatable, but often asymptomatic. New diagnostic strategies targeting healthy individuals are therefore needed. The 17 high schools in Aarhus County, Denmark, comprising 8909 students, were cluster-randomized into an intervention group which was offered examination by mailing a urine sample (males and females) and a vaginal flush sample (females) directly to the laboratory, and a control group who were offered examination by a physician. Ninety-three percent (867/928) of the sexually experienced female responders underwent examination in the intervention group, compared with 8% (63/833) in the control group (p < 0.001). The corresponding figures for males were 97%, (430/442) and 2% (4/246), respectively (p < 0.001). Also statistically significantly more infected females and males were found in the intervention group (43 females and 11 males in the intervention group vs. five females and one male in the control group). Home sampling improves the diagnosis of C trachomatis infection among apparently healthy young individuals.