Therapy with Cyclophosphamide may be effective in patients with inflammatory bowel disease and autoimmune manifestations where continued biological therapy is contraindicated. Undesirable effects of Cyclophosphamide pulse therapy have not be recorded in a small patient sample. The tested sample had markedly higher mean age of treated patients, anti-TNF therapy failure rate and significant proportion of extraintestinal manifestations. This treatment alternative deserves - in view of the limited range of immunosuppressant agents at our disposal - to be paid more attention in the clinical setting.