Branched-chain amino acids (BCAAs; valine, leucine, and isoleucine) represent important precursors in the synthesis of glutamine and alanine in the skeletal muscle. Enhanced oxidation of BCAAs can cover the elevated demands of the body on glutamine and alanine during severe illnesses (sepsis, polytrauma, burns). The sufficient supply of the BCAAs in such conditions is facilitated by increased proteolysis in skeletal muscle. However, it can result in muscle wasting and negative protein balance. While concentrations of the BCAAs and alanine are rarely significantly altered, a marked decrease in glutamine concentration, particularly in skeletal muscle, is frequently observed. Glutamine is therefore considered to be a conditional essential amino acid. The manuscript describes the metabolic relations between BCAAs and glutamine, and explains the importance of the recycling of BCAAs and their ketoanalogues between the liver and skeletal muscle. Finally, it is suggested that the favourable effect of glutamine administration on protein metabolism is related to changes in BCAA metabolism.