The energetic demands of long-distance migratory birds change drastically, depending on the stage of their life cycle. Changing demands are reflected in the up and down regulation of adipose tissue and organ mass. This paper presents new data on organ size changes during different stages of spring migration of garden warblers (Sylvia borin). Phenotypic mass changes were quantified in 13 organs of birds caught in Tanzania, Ethiopia and Egypt. We also sampled birds after a simulated stopover in Egypt. Some organs increased in mass up to about 1.5-fold during migration from Tanzania to Ethiopia, while some remained unchanged or even decreased in mass. During flight across the Sahara, nearly all organ masses including heart and flight muscles were reduced. Exceptionally large reductions (approximately 50%) were observed for liver, bile, spleen, kidney and digestive tract organs. The only exceptions were the testes, which increased 4-fold in mass. During the simulated stopover in Egypt, a significant recovery was observed for kidney, liver, heart, proventriculus, and small intestine. The testes continued to increase in mass. Flexible remodeling of organ size in the course of spring migration thus comprises significant changes for all quantified organs, with a variety of organ-specific patterns. Individual organ patterns are differentially shaped by functional aspects according to the different organ requirements in the alternation of flight and stopover phases, energetics, future demands, and protein requirements. Anticipatory mechanisms account for the size change of the testes, and we suggest the same for the kidney and the gall bladder.