Menstrual disturbances are common among female athletes, and oral contraceptives (OCs) are often recommended as estrogen substitution. However, there is little information about the effects of OC use in athletes, and there is great concern that OCs might impair physical performance. The aim of this study was to investigate the effects of OC use on body composition and physical performance in female athletes. Twenty-six endurance athletes (13 with oligo-/amenorrhea and 13 regularly menstruating athletes) and 12 sedentary controls were examined before and after 10 months of treatment with a low dose, monophasic, combined OC. Significant changes in body composition were recorded in the athletes, but not in the controls. There was an increase in weight and fat mass only in athletes with oligo-/amenorrhea. These changes were associated with a decrease in ovarian androgens. OC treatment also increased bone mineral density, with the largest increase in athletes with a low bone mineral density at baseline. Despite significant changes in body composition, little impact on physical performance was recorded. We have demonstrated that OC treatment in female athletes has predominantly beneficial effects on body composition without adverse effects on physical performance and could be used for the prevention of osteoporosis in athletic amenorrhea. However, it cannot be excluded that a marked increase in fat mass might have unfavorable effects for athletic performance in individual women.