The invention refers to an FLT3 inhibitors for immune suppression. New methods are provided for suppressing the immune system and for treating immune related disorders. Therapies of the invention include administration of an FLT3 inhibitor compound to a subject in need thereof, such as a subject suffering from organ rejection, bone marrow transplant rejection, acquired immune deficiency syndrome, arthritis, aplastic anemia, graft-versus-host disease, Graves' disease, established experimental allergic encephalitomyelitis, multiple sclerosis, lupus, or a neurological disorder. Methods are also provided for screening therapeutic agents for treating immune disorders, including the use of a mouse having an elevated level of FLT3 receptor activity.