Few studies have examined the cost-effectiveness of microsurgery, and little is known about the cost-effectiveness of flap monitoring. We studied the costs related to microsurgery during 2004 to 2006 in Kuopio University Hospital. A total of 99 patients were reconstructed with 109 flaps. Primary success was achieved in 64% of cases. Reoperation for anastomosis was conducted in 25% and for other surgical complications in 27%. The intended result was achieved in 94% of cases. The mean total cost of hospital care was 20,000 euro in head and neck cancer surgery, 15,500 euro in defects of the lower extremities, and 9200 euro in breast reconstruction. The costs were greatly influenced by surgical complications (i.e., if the primary reconstruction failed, then the secondary microvascular flap almost doubled the expense involved; mean expenses per case 27,900 euro). Microdialysis was used in flap monitoring with an additional cost of 535 euro per patient. We found that microdialysis provided an early diagnosis of perfusion failure and helped to save the flap. It was estimated that if one or two flaps per year are saved due to more effective monitoring, then the extra costs of using microdialysis are covered.