Graft-versus-host disease (GVHD) is caused by the disorder of self-tolerance mechanisms in the thymus and of peripheral tolerance mechanisms. Several cytokines also modulate GVHD, thus inducing complicated clinical features; therefore, it is important to determine which cytokines are mainly involved in the induction of GVHD in order to suppress the production of such cytokines for controlling GVHD. GVHD is closely related to immunodeficiency through T cell and B cell dysfunction. Although cytokines can potentiate these immunological dysfunction, GVHD may be simultaneously augmented by exogenous administration of cytokines. On the contrary, cytokines regulate hematopoiesis as well. Therefore, we should analyze the kinetics of cytokines and their receptor expressions as well as the influences of these factors on immune system and hematopoiesis to control GVHD and immunodeficiency.