Elite female athletes have exceptionally high physical activity levels. The physiological stresses associated with high exercise can disrupt normal homeostatic processes, altering menstrual cycles and energy balance, leading to a condition known as The Female Athlete Triad. The aim of this study was to examine bone and muscle characteristics of female elite-level endurance runners compared with age-matched controls. The study received ethical approval and all participants provided written consent. Controls (C) (n=15), eumenorrheic athletes (EA) (n=15) and amenorrheic athletes (AA) (n=14) completed dual energy X-ray absorptiometry (DEXA) and peripheral quantitative computed tomography (pQCT) scanning, three-day food diary, magnetic resonance imaging and muscle function testing. The amenorrheic athletes had 11.4% greater endochondral circumference of the radial diaphysis than controls. At the radial epiphysis EA had 14% greater total area than C, but the AA and C were similar. At the tibia diaphysis, the EA had a greater total area, cortical area and periosteal circumference than C (13.5,14.2 and 7.06% difference respectively). Similarly, the AA tibia diaphysis total area and periosteal circumference were greater than C (18 and 8.9% difference respectively), although EA had a 13.8% greater cortical thickness than AA at the tibia diaphysis. DEXA results (g/cm2) highlighted significant differences between C and AA at sites of trunk (0.91±0.16 for C vs 0.82±0.22 for AA), spine (1.05±0.24 vs 0.92±0.33) and lumbar spine (L1-4) (1.19±0.28 vs 1.04±0.33) (p<0.05). At the pelvis significant differences were found between C and EA, and between EA and AA (1.11 ±0.25 C, 1.14±0.23 EA and 0.99±0.093 AA; all p<0.05). Both the AA and EA had significantly higher energy intake per day than controls (p=0.008 and p=0.001, respectively), with a trend towards higher calorie intake in EA than AA. The AA consumed significantly less protein than C (p=0.015). The EA consumed significantly more protein (p=0.043) and more fat than C (p=0.024). Muscle size and strength were similar across all groups. These results show that amenorrheic female athletes can have wider and thinner bones than eumenorrheic athletes and controls and highlight the importance of screening for the Female Athlete Triad.