Does a Colonoscopy Show Endometriosis? What a Normal Result Really Means

If you have painful periods, pain when you open your bowels, bloating, or bleeding from the back passage, there is a good chance someone has sent you for a colonoscopy. Many women are told afterwards that everything looked normal — and are left more confused than before.

THE SHORT ANSWER

A colonoscopy usually cannot see endometriosis, and a normal result does not rule it out. In the largest study to test this directly, colonoscopy missed 92% of women who were later confirmed at surgery to have endometriosis in the bowel. That is not a failure of the doctor or the equipment. It is because of where this disease grows.

A colonoscopy is still a genuinely useful test — but for ruling other conditions out, not for finding endometriosis. Knowing the difference changes what you should ask for next.

Why do so many women with endometriosis end up having a colonoscopy?

Because endometriosis very often causes bowel symptoms — and bowel symptoms send you to a gastroenterologist.

In one study of 355 women having surgery for suspected endometriosis, 90% reported gastrointestinal symptoms. Bloating affected 83% and other bowel symptoms 71%. Yet when the surgeons looked inside, only 7.6% actually had endometriosis growing on the bowel itself. The symptoms are real. They are simply a poor guide to where the disease is.

What the research shows	The number
Women with endometriosis who report bowel or digestive symptoms	about 90%
Of those same women, how many actually had endometriosis on the bowel	7.6%
How much more likely women with endometriosis are to also be diagnosed with IBS	3.3 times
Women in one clinic who had previously been told they had IBS	21% — and 79% of them turned out to have endometriosis
Average time from first symptoms to an endometriosis diagnosis	4 to 11 years
Average number of doctors seen before diagnosis	7

Sources: Maroun 2009 (355 women) · Chiaffarino 2021 (meta-analysis of 11 studies) · Roth 2024.

Why can’t a colonoscopy see endometriosis?

Because endometriosis grows into the bowel from the outside in, and a colonoscopy camera only sees the inside.

The bowel wall has four layers. Think of it like the wall of a house: a colonoscopy sends a camera down the hallway inside, so it can inspect the wallpaper beautifully — but it cannot see what is happening in the brickwork, or in the garden outside.

Endometriosis lands on the outer surface of the bowel and burrows inward. By the time surgeons remove a piece of affected bowel and examine it under a microscope, the outer surface and the muscle layer are involved in essentially every case. The inner lining — the wallpaper, the only layer the camera can see — is involved in roughly 8 to 15% of cases.

• Caption: Figure 1. Endometriosis invades the bowel wall from the outside in. It reaches the inner lining — the only surface a colonoscopy camera can see — in only about 8 to 15% of cases.

Layer of the bowel wall	How often endometriosis reaches it	Can a colonoscopy see it?
Serosa (outer surface)	About 100%	No
Muscularis propria (muscle layer)	About 100%	No
Submucosa	24–34%	No
Mucosa (inner lining)	8–15%	Yes — sometimes

Measured in surgical specimens: Kavallaris 2003 (50 women) · Kaufman 2011 (89 women) · Tschann 2021 (25 women).

How often does a colonoscopy actually find bowel endometriosis?

About 7% of the time. In practical terms, it misses more than nine out of every ten cases.

The clearest evidence comes from a prospective study published in 2015. Researchers gave 174 women with deep endometriosis a colonoscopy first, then operated. Surgery found endometriosis in the bowel in 76 of them — nearly 44%. The colonoscopy had flagged something suspicious in just 7 women.

• Caption: Figure 2. Of 100 women with surgically confirmed bowel endometriosis, colonoscopy identified around 8. The other 92 had a colonoscopy that looked normal, or showed something that was not recognised as endometriosis.

A second study, of 79 women, found an even lower detection rate of 3%. One study using a slightly different technique reported much higher numbers, but it counted indirect signs — kinking, stiffness and pressure on the bowel from outside — rather than seeing endometriosis itself. Even in that study, visible disease inside the bowel appeared in fewer than 5% of examinations.

There is one situation where a colonoscopy earns its place as a diagnostic test: when the endoscopist can actually see an abnormal, nodular area. When a biopsy is taken from a visibly nodular lesion, it confirms endometriosis about 67% of the time. When the surface looks smooth, biopsies in one series confirmed it 0% of the time — the tissue is simply too deep for the forceps to reach.

My colonoscopy was normal. Does that mean I don’t have endometriosis?

No. A normal colonoscopy tells you very little about endometriosis.

THE MOST IMPORTANT NUMBER IN THIS ARTICLE

Among women being investigated for deep endometriosis, about 4 in 10 who had a completely normal colonoscopy still had endometriosis in the bowel when surgeons looked.

A normal colonoscopy is good news about bowel cancer and inflammatory bowel disease. It is close to meaningless as reassurance about endometriosis. If your symptoms are still there, the investigation is not finished.

There is a second, less discussed problem. When a colonoscopy does show something, endometriosis is often not what gets written on the report. In published surgical series, endometriosis in the bowel was mistaken beforehand for bowel cancer in about three quarters of cases that came to surgery, and has been reported as a polyp, an ulcer, or inflammatory bowel disease. One woman described in the literature had three separate colonoscopies with biopsies, all reported as a possible tumour, before surgery finally showed endometriosis.

So the test can mislead in both directions — falsely reassuring when it is normal, and pointing at the wrong diagnosis when it is not.

When do you still need a colonoscopy?

This section matters more than any other on this page. Everything above is about what a colonoscopy cannot do for endometriosis. None of it is a reason to skip one when there is a separate medical reason to have it.

Having endometriosis does not protect you from bowel disease. If anything, the opposite: a nationwide study of 37,661 women found that women with endometriosis were about 1.5 times more likely to develop inflammatory bowel disease, and that link was still there twenty years after diagnosis. Bowel cancer risk in women with endometriosis is not raised — but it is not lowered either, and bowel cancer is rising sharply in people under 50.

ASK ABOUT A COLONOSCOPY IF ANY OF THESE APPLY TO YOU:

• Bleeding from the back passage that is not linked to your period

• Iron deficiency or anaemia that no one has explained

• Unexplained weight loss

• A lasting change in your bowel habit that does not follow your cycle

• A family history of bowel cancer or inflammatory bowel disease

• You are at the age for routine bowel cancer screening (45 in the US, varies elsewhere)

• You are being assessed for surgery that may involve removing part of the bowel

• Symptoms of a blockage — severe cramping, vomiting, being unable to pass anything

Cyclical bleeding — bleeding that arrives with your period and settles afterwards — points towards endometriosis rather than away from it. Persistent bleeding that ignores your cycle is the pattern that needs a camera.

There is also a good argument for a colonoscopy before planned bowel surgery for endometriosis. At least one high-volume specialist centre performs a lower endoscopy in every patient before operating, to check for narrowing and to rule out anything unexpected. That is a different job from making the diagnosis.

Which tests actually find bowel endometriosis?

Specialist transvaginal ultrasound and MRI — because both look through the whole thickness of the bowel wall instead of only at the lining.

• Caption: Figure 3. Detection rates for bowel endometriosis. Expert transvaginal ultrasound finds about 91 cases in 100 and MRI about 85, compared with about 7 for colonoscopy.

Test	Finds it	What it’s good for
Specialist transvaginal ultrasound	91%	First choice. Cheap, no radiation, no preparation, done in clinic. Accuracy depends heavily on how well trained the person scanning you is.
MRI of the pelvis	85%	Excellent for mapping how big a nodule is, how much of the bowel it wraps around, and how close it sits to other organs — the measurements a surgeon needs.
Colonoscopy	7%	Ruling out bowel cancer and inflammatory bowel disease. Not a test for endometriosis.
Laparoscopy (keyhole surgery)	—	The definitive answer, and treatment at the same time. No longer needed just to make the diagnosis in most cases.

Sources: Guerriero 2016 (19 studies, 2,639 women) · Guerriero 2018 (6 studies, 424 patients) · Milone 2015 (174 women).

THE SINGLE MOST USEFUL THING YOU CAN DO

Ask who is doing your ultrasound. A standard pelvic scan and a specialist endometriosis scan are not the same examination. The 91% figure above comes from experienced operators using a specific technique for looking at the bowel and the spaces behind the uterus. A general scan reported as “normal ovaries, normal uterus” has not looked for what you need looked for.

What do the medical guidelines say?

No national or international guideline anywhere recommends a colonoscopy to diagnose endometriosis.

Most of the major guidelines simply never mention it — the recommended path runs from clinical examination to ultrasound, then MRI, then keyhole surgery if needed. The few that do mention colonoscopy say the same thing in different words.

Guideline	What it says about colonoscopy
ESHRE (Europe, 2022)	Does not mention colonoscopy at all. Recommends ultrasound or MRI, then laparoscopy if needed.
NICE (UK, updated 2024)	Does not mention colonoscopy at all. Recommends transvaginal ultrasound for everyone with suspected endometriosis.
CNGOF / HAS (France, 2018)	“Colonoscopy is not recommended as a first-line investigation when deep posterior endometriosis is suspected.”
ESGE / ESHRE / WES (2020)	Colonoscopy is indicated if there is rectal bleeding, to rule out primary bowel disease — but “does not give sufficient information” about endometriosis in the bowel wall.
German guideline (2025)	“Rectal bleeding is rare and endoscopic biopsies are often not diagnostically useful.”
SOGC (Canada, 2024)	Colonoscopy “is not required for diagnosis”, but may be warranted for persistent non-cyclical rectal bleeding or a family history of gastrointestinal cancer.

TECHNICAL SUMMARY FOR CLINICIANS

(For referring GPs, gastroenterologists, and gynaecologists)

• Diagnostic accuracy: Milone 2015 (prospective, n=174, surgical reference standard): sensitivity 7%, specificity 98%, PPV 85%, NPV 58%; 70 of 76 confirmed cases missed. Mangler 2013 (n=79): sensitivity 0.03. Lukovich 2017 (n=383) reports 96.2% sensitivity but scores indirect extrinsic signs — kinking 57%, extrinsic impression 46%, wall rigidity 38% — as positive, with intraluminal disease in only 4.9%. The target condition is not the same, and its published figures do not reconcile with its own raw counts (TP 103, FP 5, FN 8).

• Negative predictive value is the clinically operative number: At 43.6% prevalence, NPV 58% leaves roughly 42% residual probability after a normal examination. Negative colonoscopy should not be documented or communicated as excluding bowel endometriosis.

• Depth of infiltration: Serosa and muscularis propria involved in ~100% (Kavallaris 2003, n=50); submucosa 24–34%; mucosa 8–15%. Colonoscopic biopsy yield 47% overall, 67% with surface nodularity versus 0% without (Kim 2011, n=17, p=0.02).

• Colonoscopy is absent from the diagnostic accuracy evidence base by design: The Nisenblat 2016 Cochrane review (49 studies, 4,807 women) assessed TVUS, TRUS, MRI and MDCT-enema. No pooled accuracy estimate for colonoscopy exists in any meta-analysis.

• Comparators: Rectosigmoid DIE — TVUS pooled sensitivity 91% (95% CI 85–94), specificity 97% (Guerriero 2016); MRI 85% (78–90), 95% (83–99) (Guerriero 2018). The two are statistically indistinguishable (p=0.86–0.90). Neither is replaced by endoscopy.

• Retained indications: Exclusion of colorectal malignancy or IBD where independent alarm features exist; age-appropriate CRC screening on its own merits; pre-operative assessment before segmental resection. Endometriosis carries IBD SIR 1.5 (95% CI 1.4–1.7; Jess 2012, n=37,661), robust at ≥20 years and in surgically verified disease, and CRC risk that is unchanged rather than reduced (SRR 1.00, 0.87–1.16; Kvaskoff 2021). A known endometriosis diagnosis never lowers the pre-test probability of these conditions.

• Interpretive caution: Abnormal findings are frequently misattributed — 6 of 8 resection cases preoperatively called carcinoma (Jiang 2013); mucosal cases reported as adenoma and as solitary rectal ulcer syndrome; 3 of 100 consecutive resections managed as IBD until surgery (Guadagno 2015).

Questions to take to your appointment

Print this page, or photograph it. Bringing specific questions changes the conversation.

• [ ] If my colonoscopy was normal, what has that actually ruled out — and what has it not ruled out?

• [ ] Has anyone looked for endometriosis with a specialist ultrasound, rather than a standard pelvic scan?

• [ ] Who will be performing the ultrasound, and do they have specific training in scanning for deep endometriosis?

• [ ] Was the area behind my uterus and the wall of my bowel specifically examined and described in the report?

• [ ] Do my bowel symptoms follow my menstrual cycle? Has that pattern been recorded in my notes?

• [ ] If a scan does not find anything, what is the next step — and when?

• [ ] Do I have any warning signs that mean I need a colonoscopy for a separate reason?

• [ ] Should I be referred to a specialist endometriosis centre?

FIND AN ESSI SPECIALIST

Bowel endometriosis is complex, and outcomes are better in the hands of surgeons who treat it regularly. ESSI members are endometriosis surgical specialists working in centres around the world. Use the ESSI directory to find a specialist near you, or to arrange a second opinion on imaging you have already had.

[Find a specialist →]

References

1. Milone M, Mollo A, Musella M, et al. Role of colonoscopy in the diagnostic work-up of bowel endometriosis. World J Gastroenterol. 2015;21(16):4997–5001.

2. Kavallaris A, Köhler C, Kühne-Heid R, Schneider A. Histopathological extent of rectal invasion by rectovaginal endometriosis. Hum Reprod. 2003;18(6):1323–7.

3. Kaufman LC, Smyrk TC, Levy MJ, Enders FT, Oxentenko AS. Symptomatic intestinal endometriosis requiring surgical resection. Am J Gastroenterol. 2011;106(7):1325–32.

4. Kim KJ, Jung SS, Yang SK, et al. Colonoscopic findings and histologic diagnostic yield of colorectal endometriosis. J Clin Gastroenterol. 2011;45(6):536–41.

5. Mangler M, Medrano N, Bartley J, et al. Value of diagnostic procedures in rectovaginal endometriosis. Aust N Z J Obstet Gynaecol. 2013;53(4):389–94.

6. Guerriero S, Ajossa S, Minguez JA, et al. Accuracy of transvaginal ultrasound for diagnosis of deep endometriosis in uterosacral ligaments, rectovaginal septum, vagina and bladder. Ultrasound Obstet Gynecol. 2016;47(3):281–9.

7. Guerriero S, Saba L, Pascual MA, et al. Transvaginal ultrasound vs magnetic resonance imaging for diagnosing deep infiltrating endometriosis. Ultrasound Obstet Gynecol. 2018;51(5):586–95.

8. Nisenblat V, Bossuyt PMM, Farquhar C, Johnson N, Hull ML. Imaging modalities for the non-invasive diagnosis of endometriosis. Cochrane Database Syst Rev. 2016;2:CD009591.

9. Maroun P, Cooper MJW, Reid GD, Keirse MJNC. Relevance of gastrointestinal symptoms in endometriosis. Aust N Z J Obstet Gynaecol. 2009;49(4):411–4.

10. Chiaffarino F, Cipriani S, Ricci E, et al. Endometriosis and irritable bowel syndrome: a systematic review and meta-analysis. Arch Gynecol Obstet. 2021;303(1):17–25.

11. Jess T, Frisch M, Jørgensen KT, Pedersen BV, Nielsen NM. Increased risk of inflammatory bowel disease in women with endometriosis: a nationwide Danish cohort study. Gut. 2012;61(9):1279–83.

12. Kvaskoff M, Mahamat-Saleh Y, Farland LV, et al. Endometriosis and cancer: a systematic review and meta-analysis. Hum Reprod Update. 2021;27(2):393–420.

13. Jiang W, Roma AA, Lai K, et al. Endometriosis involving the mucosa of the intestinal tract: a clinicopathologic study of 15 cases. Mod Pathol. 2013;26(9):1270–8.

14. Guadagno A, Grillo F, Vellone VG, et al. Intestinal endometriosis: mimicker of inflammatory bowel disease? Digestion. 2015;92(1):14–21.

15. Tschann P, Vitlarov N, Hufschmidt M, et al. Colorectal resection in endometriosis patients. Eur J Med Res. 2021;26:12.

16. Becker CM, Bokor A, Heikinheimo O, et al. ESHRE guideline: endometriosis. Hum Reprod Open. 2022;2022(2):hoac009.

17. National Institute for Health and Care Excellence. Endometriosis: diagnosis and management. NICE guideline NG73, updated 2024.

18. Tardieu A, Sire F, Gauthier T. Diagnostic accuracy of endoscopy in endometriosis: CNGOF-HAS endometriosis guidelines. Gynecol Obstet Fertil Senol. 2018;46(3):200–8.

19. Working group of ESGE, ESHRE and WES. Recommendations for the surgical treatment of endometriosis. Part 2: deep endometriosis. Hum Reprod Open. 2020;2020(1):hoaa002.

20. Dave HB, Chamié LP, Young SW, et al. Bowel endometriosis: systematic approach to diagnosis with US and MRI. RadioGraphics. 2025;45(4):e240102.

This article is general information, not medical advice. It cannot take the place of an assessment by a clinician who knows your history. If you have rectal bleeding, unexplained weight loss, or a persistent change in your bowel habit, please see a doctor — do not use this article as a reason to delay.