Weight-bearing exercise has been recognized widely to be beneficial for long-term bone health. However inherent differences in bone-loading characteristics and energy expenditure during participation in endurance sports place many endurance athletes at a relative disadvantage with regard to bone health compared with other athletes. Adolescents and adults who participate in endurance sports, such as running, and non-weight-bearing sports, such as biking and swimming, often have lower bone mineral density (BMD) than athletes participating in ball and power sports, and sometimes their BMD is lower than their inactive peers. Low BMD increases the risk of stress and fragility fractures, both while an athlete is actively competing and later in life. This article reviews the variable effects of distance running, cycling, swimming, and triathlons on bone health; the evaluation of stress and fragility fractures; and the diagnosis, management, and prevention of low BMD in endurance athletes.