Study Objective. To estimate the recurrence rate of chocolate cysts 3 to 12 months after ablative laparoscopic surgery. The secondary outcome measure was the need for a repeat surgical procedure. Design. Prospective cohort study (Canadian Task Force classification II-2). Setting. Tertiary referral center for laparoscopic treatment of endometriosis. Patients. Seventy-three consecutive women with chocolate cysts larger than 2 cm. Intervention. Laparoscopy at which cyst capsules were vaporized or coagulated with the potassium-titanylphosphate (KTP) laser or Bicap bipolar diathermy. Measurements and Main Results. There were 96 cysts (23 bilateral) in 73 women (1 patient underwent a two-stage procedure). Their mean diameter was 4.79 cm (range 2-25 cm). The median r-AFS score was 56 (range 22-128), and 55 patients (75.3%) had stage 4 disease. The KTP laser was used in 50 women (68.5%) and bipolar diathermy in 23 (31.5%). At 12 months, 5 patients (6.9%) were lost to follow-up, and 12 had a recurrent cyst. Therefore, the cyst recurrence rate/patient was 16.4% (12/73) and the rate/cyst was 12.5% (12/96). Women who had recurrences were significantly more likely to have bilateral cysts, 7/12 (58.3%), than those with single cysts, 16/61 (26.2%, p=0.032). Bicap bipolar diathermy was associated with a recurrence rate of 20.8% (5/24). The rate in women who had KTP laser ablation was 14.3% (7/49, NS). Eighteen patients had repeat operations (including on recurrent cysts). Therefore the reoperation rate was 24.6% (18/73). No major surgical complications occurred. One woman had a postoperative wound infection after a second procedure to remove an ovary with a recurrent cyst. Conclusion. Laparoscopic cyst fenestration followed by capsule ablation is safe and effective treatment for preventing recurrence of chocolate cysts.