During endurance exercise, there is a net breakdown of body protein and the amino acids so mobilized are available for increased rates of oxidation and gluconeogenesis. At least part of the net loss of protein is due to a decrease in the rate of protein synthesis during exercise. Liver protein degradation is increased during exercise as a result of autophagy and proteolysis of cell material inside the secondary lysosomes. The rate of degradation of contractile proteins is decreased during exercise but is increased during the recovery period if the exercise is of high intensity and of long duration. Preliminary evidence suggests that the rate of degradation of non-contractile proteins in muscle may be increased at the same time that contractile protein degradation is decreased.