The relationship between resting thyroid hormone concentrations and exercise muscle metabolism was examined among eumenorrheic endurance-trained (n = 11), amenorrheic endurance-trained (n = 8), and eumenorrheic nonathletic (n = 13) subjects. Muscle metabolism was assessed with 31Phosphorous magnetic resonance spectroscopy by measuring changes in phosphocreatine (PCr), inorganic phosphate (Pi), and pH during plantar flexion exercise and recovery. All groups had similar Pi/PCr ratios and pH changes during exercise. Eumenorrheic endurance-trained subjects had faster recovery rates for PCr and Pi/PCr following exercise compared to the nonathletes (p < .05) and faster recovery rates for PCr compared to amenorrheic subjects (p < .05). Thyroxine (T4) and triiodothyronine (T3) levels were significantly lower in amenorrheic subjects compared to both eumenorrheic groups (p < .05). It was concluded that routine training enhances muscle metabolism, as measured by phosphate recovery kinetics. This enhancement was not evident in amenorrheic athletes with reduced T3 and T4 concentrations.