Objective: A bipolar radio-frequency impedance-controlled endometrial ablation system is more effective than balloon ablation in the treatment of dysfunctional uterine bleeding. The aim of the present study was to compare the costs of both treatments, and to perform a cost-effectiveness analysis. Study design: An economic evaluation was set up alongside a randomised clinical trial comparing bipolar radio-frequency endometrial ablation and balloon ablation in 126 patients with dysfunctional uterine bleeding. Data on resources used for treatment and lost production time were prospectively collected, and costs of both treatments were calculated. Results: Mean direct medical costs per patient were €1638 for bipolar ablation and €1545 for thermal balloon ablation with a mean difference of €93 (95% CI €45-140, P-value 0.01). Mean indirect medical costs were just over €200 in each group. Incorporation of the costs of post-ablation hysterectomies resulted in mean costs of €2006 and €2053 in the balloon group (P-value 0.01). In the balloon group, the cost per satisfied patient was €2333 compared to €2112 in the bipolar group. Similarly, in the bipolar group the cost per amenorrhoeic patient was €4361 and in the balloon group €12831. Conclusions: The direct costs of bipolar ablation were higher than the costs of balloon ablation. However, after inclusion of the retreatment costs, bipolar ablation was less expensive than balloon ablation.