Since the early 1960s it has been held that migrating birds deposit and use only fat as fuel during migratory flight, with the non–fat portion of the body remaining homeostatic. Recent evidence from field studies has shown large changes in organ sizes in fuelling birds, and theory on fuel use suggests protein may be a necessary fuel during flight. However, an absence of information on the body condition of migrants before and after a long flight has hampered understanding of the dynamics of organs during sustained flight. We studied body condition in a medium–sized shorebird, the great knot (Calidris tenuirostris), before and after a flight of 5400 km from Australia to China during northward migration. Not only did these birds show the expected large reduction in fat content after migration, there was also a decrease in lean tissue mass, with significant decreases in seven organs. The reduction in functional components is reflected in a lowering of the basal metabolic rate by 46%. Recent flight models have tried to separate the ‘flexible’ part of the body from the constant portion. Our results suggest that apart from brains and lungs no organs are homeostatic during long–distance flight. Such organ reductions may be a crucial adaptation for long–distance flight in birds.