Immunosuppressive treatment in inflammatory bowel disease (IBD) is an important and often the fundamental part of therapy. Glucocorticoids should not be used in long-term treatment because of their side effects and, otherwise, poor efficiency in a subgroup of patients. Purine analogues (azathioprine and 6-mercaptopurine) comprise another group of immunosuppressive drugs. They are the principal drugs in the majority of patients with Crohn’s disease and steroid-dependent or steroid-resistant patients with ulcerative colitis. However, in about 20% of IBD patients purine analogues are ineffective and in a similar percentage of patients they are responsible for side-effects, leading to withdrawal of treatment. Biological therapy or surgery is usually considered in these patients, not commonly taking into account the third option of immunosuppressive treatment – methotrexate (MTX). This drug, widely used for many years in patients with severe rheumatoid arthritis and psoriasis, is relatively seldom used in gastroenterology. This paper discusses mechanisms of action of MTX, its dosage and safety of treatment and presents the results of its use in patients with IBD.