This study compared the cost and time involved of helium thermal coagulator (HTC) treatment with medical therapy using gonadotrophin-releasing hormone analogues in women with minimal to moderate endometriosis. In a prospective randomised controlled trial, 35 women with history of pain were, upon confirmation of minimal to moderate endometriosis at diagnostic laparoscopy, randomised to immediate surgical or medical treatment. They were asked to complete analogue pain score sheets, and their symptoms were reviewed before treatment and at 3, 6, and 12 months after treatment. The cost of the medical or surgical treatment was evaluated from the time of diagnosis to the time of cure or symptom relief. The average cost per Helica probe is £111.81 with the machine on free loan, and the total cost of a 6-month course of injectable Zoladex with add-back therapy is £811.92. The costs involved in the two treatment modalities were analysed using the Mann-Whitney test; a p-value <0.05 was considered significant. In the medical group, three women out of 18 were symptom-free, 11 required surgical treatment of endometriosis, one had a laparoscopically-assisted vaginal hysterectomy, and three became pregnant before their final reviews. In the surgical group, nine women were symptom-free at the end of 12 months, four required Zoladex therapy, one required oral contraceptive pills, and three required repeat surgical treatment. The average cost per patient in the surgical arm was £323.29 and in the medical arm was £918.12 (p<0.0001). Mean operating times in the surgical and medical arms were 32.35 min and 20.83 min, respectively. This suggests that when facilities and expertise are available, it is better to see and treat mild to moderate endometriosis. There were no surgical complications in our series. Surgical treatment with HTC therapy is safe and is a cheaper and more effective therapy. This is the first study that has looked at the cost-effectiveness of HTC therapy in managing mild to moderate endometriosis.