BACKGROUND: Iron deficiency and anaemia (Hb-level<12g/dl) is common in patients with inflammatory bowel disease (IBD). First line treatment for correcting iron deficiency is oral iron. In patients intolerant to oral iron, intravenous (IV) iron is recommended. OBJECTIVES: To evaluate incremental costs and effects (ICER) of IV iron compared to discontinuation of oral iron, in IBD patients intolerant to oral iron. METHODS: A micro-simulation model of the Hb-level and intravenous or oral iron treatment was developed using published data, a chart review of IBD patients and calibration. QALYs and costs for drug (including administration), transport and loss of production due to IV iron administration in an outpatient setting were estimated using a one-year time frame with two relapses causing anaemia. At treatment start, patients are in relapse with a Hb-level of 10 g/dl and treated with oral iron. As they become intolerant, the model either switches them to IV iron or discontinues treatment. Sensitivity analyses were carried out with respect to initial Hb and number of relapses per year. RESULTS: In the base case, treatment with IV iron generates a QALY gain of 0.0334 at a cost of €1,530, i.e. an ICER of €45,800. A treatment start at lower initial Hb-levels generates higher QALY-gains and lower costs per QALY, e. g. €35,900 per QALY gained with an initial Hb-level of  9 g/dl. The ICER in patients with one relapse per year gain is €61,460, reflecting a high initial cost when determining appropriate iron treatment regimen. CONCLUSIONS: In a health care perspective, IV iron compared to oral iron is cost-effective in patients in relapse. In a societal perspective, IV iron is cost-effective provided that <50% of the patients work during relapse.