Adverse drug reactions frequently involve the gastrointestinal tract. We present two cases of colitis that occurred months to years after chemotherapy and autologous stem cell transplantation for the treatment of lymphoma. Laboratory tests revealed altered immune status with decreased CD4/CD8 ratio and hypogammaglobinemia (in one patient). The patients had no history of inflammatory bowel disease or immunodeficiency. Biopsies showed chronic active colitis with crypt architectural distortion, erosions, and ulcers as well as pyloric gland metaplasia and loss of plasma cells (in one patient, respectively). Colitis appeared to be related to lymphoma therapy, but could not be attributed to a distinct drug or infectious agent, suggesting the concept of persistent immune dysregulation driving mucosal inflammation. Hence, we suggest “immune dysregulation-associated colitis” (ID-colitis) as an umbrella term for cases of chronic colitis, in which immune dysfunction is evident from blood samples or clinical information and inflammatory bowel disease has been ruled out.