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Background: Studies have suggested that exercise programs can reduce the incidence of noncontact injuries of the anterior cruciate ligament in female athletes. We conducted a two-year prospective study to assess the effects of a knee ligament injury prevention exercise program on the incidence of noncontact anterior cruciate ligament injuries in high-school female athletes. Methods: A prospective cohort design was used to study high-school female athletes (playing soccer, basketball, and volleyball) from fifteen schools (112 teams) for two consecutive seasons. The schools were divided into treatment and control groups. The treatment group participated in a plyometric-based exercise program twice a week throughout the season. Practice and game exposures and compliance with the exercise program were recorded on a weekly basis. Suspected noncontact anterior cruciate ligament injuries were confirmed on the basis of the history as well as at the time of surgery and/or with magnetic resonance imaging. Results: A total of 1439 athletes (862 in the control group and 577 in the treatment group) were monitored. There were six confirmed noncontact anterior cruciate ligament injuries: three in the treatment group, and three in the control group. The incidence of noncontact anterior cruciate ligament injuries per 1000 exposures was 0.167 in the treatment group and 0.078 in the control group, yielding an odds ratio of 2.05, which was not significant (p > 0.05). Conclusions: Our results suggest that a twenty-minute plyometric-based exercise program that focuses on the mechanics of landing from a jump and deceleration when running performed twice a week throughout the season will not reduce the rate of noncontact anterior cruciate ligament injuries in high-school female athletes. Level of Evidence: Therapeutic Level II. See Instructions to Authors for a complete description of levels of evidence.