An economic evaluation of intensity modulated radiotherapy (IMRT) in head and neck cancer was carried out to assess the cost of treatment and compare it to reimbursement paid to hospitals in the French Prospective Payment System. Planning required in average 20 hours of work for the physician and 6 hours for the radiation oncologist. Radiation consisted of 33 fractions in average and required 29 hours of work for the radiotherapy technician, 8 hours for the physician and 3 hours for the radiation oncologist. Mean cost of IMRT treatment was estimated at euro 10,916 (euro 2,773 for planning and euro 8,143 for radiation). The variability of costs was important and was in a large extent attributable to learning effects. As more patients were treated, unit cost of treatment was decreasing. In the French Prospective Payment System, mean reimbursement of IMRT was euro 6,987. For 70 % of the patients, reimbursement did not offset the cost of treatment. A financial support for hospitals implementing the technique is essential during the whole learning period.