More than 40,000 allogeneic hematopoietic stem cell transplants are carried out worldwide every year, mostly for patients suffering from leukemia or other diseases of the hematopoietic system. Very often, the so-called graft-versus-host reaction occurs, an inflammatory disease that can affect different organs and is caused by an unwanted defense reaction of the donor cells and the body’s own T cells. Scientists now show how these endogenous, tissue-derived T cells enter other organs, such as the intestine, via the blood and contribute to inflammation there. The study provides important approaches to better therapy in stem cell transplantation and new diagnostic options.