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Study Objective To compare the cost-effectiveness of ultrasound (US)-guided aspiration and ethanol sclerotherapy versus laparoscopic surgery for benign-appearing ovarian endometrioma. Design Prospective, cohort pilot study. Setting Multiple centers, Spain. Patients Forty patients with suspected ovarian endometrioma identified by US, with a maximum diameter of 35 to 100 mm, of whom 33 met inclusion criteria. Interventions The study group (n = 17) underwent US-guided aspiration plus sclerotherapy with ethanol, and the control group (n = 14) underwent laparoscopic cystectomy. Measurements and Main Results Recurrence, complications, and direct costs were compared. One of 17 sclerotherapy patients recurred (5.9%) compared with 4 of 14 laparoscopic surgery patients (28.6%) (odds ratio 0.18, 0.01–1.53). No serious adverse effects (Clavien-Dindo ≥ III) were observed in the sclerotherapy group; 1 patient in the surgery group had a Clavien-Dindo IIIb complication. Median hospital direct costs were significantly lower in the sclerotherapy group than those in the surgery group—266 euros versus 2189 euros. Conclusion Ethanol sclerotherapy seems to be cost-effective for endometrioma and also appears to reduce complications. In this pilot study, recurrence was not higher than with conventional surgery.