Methotrexate is an immunosuppressant that may be useful in several clinical scenarios in inflammatory bowel disease. In this article, we review the available evidence in Crohn's disease and ulcerative colitis and establish general recommendations for its use in clinical practice. Although the available data are limited, it is very likely that methotrexate is underused because its effectiveness is underestimated and its toxicity is overestimated. Both in induction therapy and in maintenance of remission, methotrexate is useful in Crohn's disease. When prescribed in combination with biologic agents, immunogenicity is less frequent and consequently long-term response could potentially be improved. There are few published studies, but several data suggest that methotrexate could also be useful in ulcerative colitis. Although myelotoxicity and liver toxicity are well known risks, methotrexate is a drug that is well tolerated in many patients, even in the long term.