Allogeneic hematopoetic stem cell transplantation often presents the only chance for cure in a number of malignant and nonmalignant hematologic diseases. However, its beneficial effects are counterweighed by the development of potentially lethal complications, most importantly the development of acute and chronic graft-vs.-host disease (GVHD). Alloantigen-reactive immune responses mediate injury and destruction of GVHD target organs, including the gastrointestinal tract, the liver, the skin, and the lung. Donor leukocyte infiltration into the respective tissues is orchestrated by interactions between chemokines and chemokine receptors, which will be reviewed using a basic science - clinical comparative approach.