Endometriosis surgery: excision, deep disease and ovarian preservation
Key Takeaways
Surgery is discussed for pain, to protect an organ, or sometimes for a pregnancy plan. A finding on a scan is not enough on its own. Taking out an ovarian chocolate cyst before IVF as a routine step has not been shown to lead to more live births. It can also lower ovarian reserve.
Key evidence: ESHRE guideline: endometriosis (2022) Bendifallah et al. — colorectal surgery complications (2021)
Surgery can be offered to ease pain, to protect an organ, or, in some situations, to help a pregnancy plan. Those aims do not always lead to the same operation.
Reading “deep endometriosis” on a report can be frightening. It does not mean an operation is urgent, or that it will help. The discussion is about what the lesions are doing, which treatments you have already tried, and what you want from care.
Why operate — and why not routinely
An operation is one option among others, not a default next step.
The ESHRE 2022 guideline places surgery among the options for pain. The choice is made with you, weighing expected benefit, side effects of medical treatment and surgical risk. Hormonal treatment suits some people; for others it fails, is poorly tolerated, or does not fit a pregnancy plan.
A blockage that threatens a kidney, or a cyst with a suspicious appearance, needs a specific assessment. The size of an endometrioma (an ovarian “chocolate cyst”) or visible adhesions do not, on their own, make surgery automatic.
Laparoscopy — surgery through small abdominal cuts — still has a diagnostic role in some cases. A normal scan does not rule out every form of endometriosis. ESHRE notes that laparoscopy can be considered if imaging is negative or if treatment started without a confirmed diagnosis (empirical treatment) has failed or is unsuitable. It is neither mandatory nor ruled out in principle.
Removing one ovary, or both, is not part of routine endometriosis surgery when you still want a pregnancy. ESHRE allows clinicians to consider hysterectomy, with or without the ovaries, in people who no longer wish to conceive and in whom more conservative treatment has failed. Hysterectomy does not necessarily cure the symptoms or the disease.
Our endometriosis guide explains the different forms of the disease and how they are assessed.
Superficial lesions: excision or ablation?
Excision cuts the lesion out. Ablation destroys it in place, for example by coagulation or vaporisation. For superficial peritoneal disease — implants on the thin lining of the pelvis — neither technique guarantees a better result in every case.
ESHRE allows clinicians to consider excision rather than ablation to reduce pain. That is a weak recommendation. It is not a rule that every patient must have excision.
In the randomised trial by Healey and colleagues, people were assigned by chance to one technique or the other. Both groups reported less pain over five years. Excision had an advantage for deep pain during sex. That result does not prove superiority for every kind of pain, for recurrence or for fertility.
Excision does let the laboratory examine the tissue that was removed. That can refine the diagnosis. It is not a guarantee of cure. Risk to nearby tissue also depends on where the lesion sits, how it is dissected and which energy is used.
Deep endometriosis: preparing surgery with a specialist team
Deep endometriosis can involve tissue under the peritoneum — the thin membrane lining the abdomen — and reach a neighbouring organ. If surgery is being considered, the first task is to map how far the disease goes and what it is doing.
The ESGE–ESHRE–WES recommendations on deep surgery describe that preparation: suitable imaging, assessment of the organs involved and organisation of the team. They rest largely on specialist experience, because comparative trials remain limited.
A specialist ultrasound and, when needed, an MRI help to locate the lesions. A colorectal surgeon or a urologist may join the planning and the operation when the lesions require it; the full team is not needed for every procedure.
Before the operation you should understand the planned procedure, the alternatives, and what might lead the team to change course during surgery.
Bowel endometriosis: shaving, disc or resection
Bowel involvement does not automatically mean a segment of intestine will be removed. The choice depends on how deep and how wide the nodules are, where they sit, and whether the bowel is narrowed.
The three main techniques are:
- Shaving: the lesion is taken off the bowel wall with the aim of not opening the bowel. An accidental opening can still happen and may need repair.
- Discoid excision: a small full-thickness disc of wall is removed, then the opening is closed.
- Segmental resection: a length of bowel is removed and the two ends are joined. There is no standard length that fits every patient.
The combined analysis of several studies by Bendifallah and colleagues, published in 2021, associates shaving with fewer rectovaginal fistulas than the other two techniques. The patients and lesions being compared are not necessarily equivalent. These data do not prove identical pain relief, nor that shaving is best in every case.
The same study does not show a statistically established difference in bladder-emptying problems in the first 30 days between shaving and segmental resection. It does not allow a promise that lasting urinary problems will be reduced.
A useful question in clinic is: “Why does this technique fit my disease, and what are its risks in my case?”
Urinary tract: bladder and ureters
Bladder disease and ureteral disease are not the same problem. The ureter carries urine from the kidney to the bladder. Obstruction can threaten the kidney even when pain is modest.
For the bladder, the discussion depends on symptoms and how deep the lesion is. If a portion of wall is removed, a catheter may be needed while it heals. The team sets the duration according to the operation performed.
For the ureter, freeing the duct — ureterolysis — can be enough when the disease is mainly outside the wall. Resection with repair or reimplantation may be needed in other cases. The choice depends on where the obstruction sits, the state of the wall and kidney function.
The ESGE–ESHRE–WES surgical recommendations set out these options. An internal “double J” stent can help in selected cases rather than as a default step.
Diaphragmatic and thoracic endometriosis
Period-related shoulder pain or cyclic chest symptoms can justify a specialist work-up, and endometriosis is not the only possible cause.
Sudden chest pain or acute shortness of breath needs urgent assessment, without waiting for the next period. One possible cause is a pneumothorax: air around the lung, which can then collapse.
ESHRE recommends specialist discussion for extra-pelvic disease. Tests are chosen according to the symptoms, and if thoracic surgery is indicated it is planned with the relevant specialists for that person.
Surgical energy and protecting tissue
The name of an instrument does not tell you whether an operation is safe. Laser, plasma and electrical instruments have different uses, and each requires control of the effect on nearby tissue.
Near an ovary, the aim is to limit the loss of healthy tissue and heat injury. Coagulation may still be needed to stop bleeding, and no device name guarantees that fertility will be preserved.
The ESHRE recommendations on endometrioma surgery stress reducing ovarian damage. It is more useful to discuss the planned procedure and its limits than to choose an operation by the brand of the technology.
Ovarian preservation techniques
Operating on an endometrioma can reduce ovarian reserve. That does not mean every operation prevents pregnancy. The risk still belongs in the decision, especially if both ovaries are involved or have already been operated on.
Cystectomy removes the cyst wall. It can also take healthy ovarian tissue with it. Ablative techniques treat the wall in place. Their benefits and limits need to be discussed for your situation. For that choice in more detail, see our article on endometriomas before IVF.
AMH (anti-Müllerian hormone) and the antral follicle count are markers of ovarian reserve. They are not an exact count of remaining eggs, and they are not a direct measure of the chance of birth. The ASRM opinion on ovarian reserve tests should be read with age and the rest of the fertility work-up.
Evidence box: plasma energy and ovarian suture studies
The study by Hurni and colleagues (2026) compared plasma energy ablation with cystectomy in 176 women aged 18 to 40 who had surgery for an endometrioma on one ovary, in a single centre. It was retrospective: treatment was not randomly assigned. The plasma-treated group had a smaller fall in AMH and more favourable antral follicle counts than the cystectomy group. Recurrence at four years was not statistically different. That is not proof the techniques are equivalent, and the study cannot show an increase in live births (babies born alive).
The retrospective study by Lin and colleagues compared robotic-assisted approximation of ovarian tissue with conventional laparoscopy in 154 patients. It does not simply compare “sutures versus cautery”. At three years, 27.5% of the robotic group and 44.7% of the conventional group were classed as having diminished reserve. These figures are shares of patients, not the percentage of eggs lost. The results are not enough to isolate the effect of suture or to recommend the robot for every patient.
Surgical risks and preventing recurrence
Risks differ widely between a limited peritoneal operation and surgery that includes a bowel or urinary procedure. The team should explain the ones that match the operation being considered.
They include bleeding, infection, adhesions, a drop in ovarian reserve and injury to a neighbouring organ. Some operations also carry a risk of fistula — an abnormal connection between two organs — or difficulty passing urine. Those complications can sometimes need another operation, as the deep-surgery recommendations note.
What follow-up after the operation?
Pain can persist or return, and new lesions can be found. Those events are not interchangeable. A recurrence percentage only means something if you know what was measured, in whom, and over how long.
If you do not want a pregnancy immediately, hormonal treatment after surgery can be offered. NICE recommendations on treatment after surgery suggest considering it to prolong the benefit of surgery on symptoms. After surgery for an endometrioma, ESHRE recommends long-term hormonal treatment to reduce the risk of the cyst coming back. The choice depends on your preferences, tolerance and contraindications; neither guideline justifies the same prescription for everyone.
A hormonal treatment meant to suppress cycles is not prescribed solely to improve a future spontaneous pregnancy: NICE notes that it does not improve spontaneous pregnancy rates. Follow-up should stay coherent with your plan for a child. Our page on endometriosis pain treatment sets out the medical options.
Surgery and a pregnancy plan: deciding the order
Relieving pain and raising the chance of pregnancy are two different aims. A procedure that helps one does not necessarily help the other.
For superficial stage I or II endometriosis associated with infertility, surgery can be discussed to improve the chance of an ongoing spontaneous pregnancy. For deep disease, the reproductive benefit of surgery remains uncertain. The ESHRE recommendations on endometriosis-associated infertility ask for an individual decision.
After surgery, the EFI (Endometriosis Fertility Index) can help estimate the chance of pregnancy without IVF. It includes operative findings. It is not calculated from an MRI alone. It does not announce a guaranteed birth rate and it does not replace the couple’s work-up.
Before IVF, routine surgery for an endometrioma is not recommended. Benefit for live birth — a baby born alive — has not been shown, and the operation can reduce ovarian reserve. Pain or difficult access to follicles at egg collection can still make an operation worth discussing. A suspicious image needs its own diagnostic assessment.
Low reserve, disease in both ovaries or another ovarian operation can lead to a discussion of egg or embryo freezing. That is not an automatic step. Its value depends on age, remaining reserve, the plan and how long you can wait. ESHRE underlines that the real benefit of this preservation in endometriosis remains uncertain.
Dr. Aksoy’s Approach before IVF
When pain is controlled, Dr. Aksoy sees two main reasons to offer surgery before IVF: imaging that raises a suspicion of malignancy, or a mass that makes it unsafe to reach the follicles.
Deep endometriosis that threatens the ureter, the bowel or kidney function also takes priority. Without those findings, he does not recommend operating routinely on an endometrioma, because of the risk to ovarian reserve.
This summary restates his answer of 13 September 2026. It describes his clinical reasoning and does not replace an individual assessment.
Key questions for your surgical consultation
The aim is to leave with a plan you understand, including the period after the operation. You can ask:
- What exact problem is the operation meant to solve, and what are the alternatives?
- What benefit can I expect for pain, and what benefit for my pregnancy plan?
- Which organs are involved, and which specialists will take part if needed?
- Why is this technique suited to my lesions? In what circumstances could it change?
- What is the risk to my ovaries, and should fertility preservation be discussed?
- What follow-up and what treatment, if any, are planned, and how long should I wait before trying to conceive?
Frequently Asked Questions for Dr. Aksoy
When do you remove an ovary during endometriosis surgery?
In endometriosis surgery I prefer to conserve the ovaries whenever I can. Finding an endometrioma — a chocolate cyst — on the ovary does not mean the ovary has to come out. Most of the time we can remove the cyst and keep healthy ovarian tissue. That operation can still harm ovarian reserve. I am especially careful in women who are young, who have not had a child yet, or who want a pregnancy later.
When do we consider removing the ovary? For example, when there is a very large, recurrent endometrioma that has destroyed a large part of the ovarian tissue, and especially if the woman no longer wants a pregnancy. Another important situation is imaging that raises a suspicion of cancer. Then our approach changes completely, and we decide with a gynaecological oncologist if needed.
In women approaching menopause who have already had several operations and whose severe pain continues, we can also discuss more extensive surgery. Removing both ovaries is a much bigger decision. In a woman who has not yet reached menopause, it causes sudden surgical menopause. That can have long-term effects on bone, heart and blood vessels, and quality of life. Removing the ovaries does not even guarantee that all endometriosis-related pain will go.
The basic question for me is this: is the benefit of taking the ovary really greater than the benefit of keeping it? If that answer is not clear, especially in women who want to protect their fertility, I first consider ovary-sparing methods.
How does recovery after laparoscopy differ between superficial disease and bowel or urinary surgery?
I tell patients that laparoscopy on its own does not mean a small operation. The cuts on the abdomen may be small, but the extent of what we do inside can change the recovery completely.
If we have only removed a few superficial peritoneal implants, recovery is usually quite fast. Most patients can go home the same day or the next day. Mild pain, bloating and tiredness in the first few days are normal. Patients can usually return to their daily activities to a large extent within one or two weeks.
Deep endometriosis is different. If the bowel, bladder or ureters — the tubes that carry urine from the kidney to the bladder — are involved, a much more extensive operation may be needed.
Removing a lesion from the bowel surface is not the same as cutting out a bowel segment and joining the ends again. After a bowel resection, diet, return of bowel movements and return to daily life can take longer. In those patients I expect four to six weeks of recovery, sometimes longer.
When we operate on the urinary tract, a catheter or a ureteric stent may be needed for a time. So we check not only that pain is easing, but also that bladder and bowel function are returning to normal.
That is why I think it matters to plan deep endometriosis operations with a general surgeon and a urologist when needed.
Recovery from the operation and the endometriosis pain fully going away are also not the same thing. Surgical healing may be complete in a few weeks, while chronic pelvic pain can take longer to settle.
The most important message I give patients is this: do not judge how large the operation was by the length of the scars on the abdomen. What matters is which organs were operated on inside.
If pain continues after surgery, when do you consider another operation?
First, I explain that continuing pain does not always mean endometriosis was left behind or has come back. In the first weeks after surgery there can be pain from the tissues healing. But if the pain is steadily increasing, or if fever or other symptoms come with it, we do not treat that as normal recovery; we look for a surgical complication.
If the healing period is over and the old pain continues, the first thing I do is not to plan another operation straight away. I review the operation report: which lesions were removed, where disease was left, and how much was done on the bowel or urinary tract.
Then I reassess the patient. If needed we look for remaining or recurrent endometriosis with ultrasound by an experienced clinician, or with pelvic MRI.
Pain can continue even when imaging shows no clear problem. Long-standing endometriosis pain does not come only from the lesions. Spasm in the pelvic-floor muscles, sensitised nerves, adenomyosis, and other bladder or bowel problems can also contribute.
So in some patients hormonal treatment, pelvic-floor physiotherapy or pain-management approaches can help more than another operation.
When do I consider operating again? If imaging shows clearly recurrent or residual disease, if pain still seriously impairs quality of life despite appropriate treatment, and if we have identified a concrete cause that surgery could correct, I may reconsider surgery.
Apart from that, situations such as kidney damage from ureteric obstruction, a serious bowel stricture, or a suspicious mass can make surgery a higher priority regardless of how severe the pain is.
I am especially careful about repeat surgery in women who have already had an endometrioma removed. Each new operation can harm ovarian reserve a little more.
My approach is not to operate again and again because the pain continues. I first try to understand why the pain is continuing. I recommend another operation only if there is a clear problem surgery can correct, and if the expected benefit outweighs the risks.
Sources
- Becker CM, Bokor A, Heikinheimo O, et al. ESHRE guideline: endometriosis. Human Reproduction Open. 2022;2022(2):hoac009. DOI: 10.1093/hropen/hoac009.
- National Institute for Health and Care Excellence. Endometriosis: diagnosis and management — NG73, recommendations. Recommendations on diagnosis, surgery and postoperative treatment; consulted 13 September 2026.
- Healey M, Cheng C, Kaur H. To excise or ablate endometriosis? A prospective randomized double-blinded trial after 5-year follow-up. Journal of Minimally Invasive Gynecology. 2014;21(6):999–1004. DOI: 10.1016/j.jmig.2014.04.002.
- Bendifallah S, Puchar A, Vesale E, Moawad G, Daraï E, Roman H. Surgical Outcomes after Colorectal Surgery for Endometriosis: A Systematic Review and Meta-analysis. Journal of Minimally Invasive Gynecology. 2021;28(3):453–466. DOI: 10.1016/j.jmig.2020.08.015.
- Working group of ESGE, ESHRE and WES. Recommendations for the surgical treatment of endometriosis Part 2: deep endometriosis. Facts, Views & Vision in ObGyn. 2020;11(4):269–297. PMID: 32322824.
- Hurni Y, La Torre F, Barbany-Freixa N, et al. Plasma energy ablation versus cystectomy in fertility-sparing surgery for endometriomas: impact on recurrence and ovarian reserve. Reproductive BioMedicine Online. 2026;52(6):105409. Published online in 2025. DOI: 10.1016/j.rbmo.2025.105409.
- Lin C, Chen G, Wang M, Zhai C, Hong ST, Chae HS. Robotic assisted versus conventional laparoscopic ovarian suture reapproximation in ovarian cystectomy of ovarian endometriomas in preserving ovarian reserve. Journal of Robotic Surgery. 2026;20:138. DOI: 10.1007/s11701-025-03089-4.
- Practice Committee of the American Society for Reproductive Medicine. Testing and interpreting measures of ovarian reserve: a committee opinion. Fertility and Sterility. 2020;114(6):1151–1157.
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The content has been created by Dr. Senai Aksoy and medically approved.