Immunosuppressive agents have become an established part of the therapeutic armamentarium for inflammatory bowel disease (IBD). However, when used in transplant recipients or for other indications, agents that suppress or modulate the immune system (immunomodulators) have been associated with an increased risk of lymphoma. Fortunately, in part because of the lower doses used in IBD patients, the risk of lymphoma in IBD patients appears to be significantly less than that associated with renal and hepatic transplant-related immunosuppression. Whether the risk of azathioprine or 6-mercaptopurine associated lymphoma in IBD is real or relates to the underlying disease remains unclear. The results of several recent large well designed population-based studies suggest that the lymphoma risk associated with azathioprine and 6-mercaptopurine therapy is likely to be of minimal clinical significance compared to the established and more frequent risks of myelosuppression and infection, and is far outweighed by the clinical benefit of immunomodulator therapy in IBD. While the issue of lymphoma risk is likely to become more relevant with the growing number of biologic and immunomodulators being tested in clinical trials for IBD, early post-marketing surveillance data on infliximab suggests that the lymphoma risk may not be any greater than that associated with azathioprine and 6-mercaptopurine.