What Is Bowel Endometriosis?

Endometriosis is a disease in which tissue similar to the lining of the uterus grows outside the uterus. Most people have heard of endometriosis as a cause of painful periods. Fewer people know that endometriosis can invade the bowel — the intestines, the rectum, the sigmoid colon — and cause symptoms that are routinely mistaken for irritable bowel syndrome, hemorrhoids, or inflammatory bowel disease.

Bowel endometriosis is not a separate disease from endometriosis. It is a particularly deep and invasive form of it. It is classified under the broad category of deep infiltrating endometriosis (DIE) — meaning that instead of sitting on the surface of nearby tissues, the lesion penetrates into and through the wall of the intestine, in some cases to a depth of several millimeters or more.

Bowel endometriosis affects roughly 10 to 12 percent of all women with endometriosis. The rectum and sigmoid colon are the most frequently involved segments, accounting for the vast majority of cases. The appendix, small bowel, and cecum can also be involved, though less commonly.

Because the symptoms of bowel endometriosis mirror so many other common digestive conditions — and because many clinicians are not trained to recognize it — the average time from first symptoms to correct diagnosis is seven to ten years. That is not acceptable. This article is written, in part, to help change that.

What Bowel Endometriosis Feels Like

The symptoms of bowel endometriosis tend to follow the menstrual cycle. That is the single most important clue: if your gut symptoms are cyclical — reliably worse around your period and better at other times — bowel endometriosis must be considered.

The most characteristic symptoms:

– Painful bowel movements during your period (dyschezia). This is one of the most specific symptoms and is frequently underreported, because patients assume it is normal or are embarrassed to mention it.

– Rectal pain during menstruation — a deep, boring, or cramping pain felt inside the rectum or lower pelvis during the period.

– Bloating and abdominal distension after meals, often worsening in the days before and during the period.

– Diarrhea during the period, sometimes alternating with constipation at other cycle phases.

– Blood in the stool during menstruation — in rare cases where endometriosis has penetrated through the full bowel wall thickness. When this occurs, it is highly specific for bowel endometriosis.

– Cramping after eating, caused by the lesion irritating or partially obstructing the bowel wall.

Common but less specific symptoms:

– Painful intercourse, particularly with deep penetration

– Chronic pelvic pain that worsens before menstruation

– Fatigue and malaise during flares

– Painful urination if endometriosis also involves nearby urinary structures

Why Symptoms Are So Often Misattributed

The gut symptoms of bowel endometriosis are nearly identical to those of irritable bowel syndrome (IBS). The critical difference is timing: IBS is not reliably cyclical with the menstrual cycle; bowel endometriosis is. Many patients carry an IBS diagnosis for years before the true cause is identified. Hemorrhoidal bleeding and inflammatory bowel disease are other frequent misdiagnoses.

If you have been told you have IBS and your symptoms are significantly worse during your period, please ask your gynecologist to evaluate you for deep endometriosis.

How Bowel Endometriosis Is Diagnosed — and Why the GI Specialist Is Usually the Wrong First Stop

The fundamental problem: this disease lives in the wall, not on the surface.

Bowel endometriosis is a disease of the bowel wall. The endometriotic lesion grows from the outside of the intestine inward — from the outer serosal surface into the muscle layer, and in severe cases into the submucosal layer beneath the inner lining. In the large majority of cases, it never reaches the inner mucosal surface of the bowel at all. The surface that a colonoscope sees is the mucosa. Which means that a colonoscopy — no matter how skilled the endoscopist — is looking at the wrong surface.

This is not a theoretical point. A 2015 prospective study in the World Journal of Gastroenterology (Milone et al.) enrolled 174 women with imaging-confirmed deep pelvic endometriosis and performed both colonoscopy and surgery on each. Among the 76 women found at surgery to have intestinal endometriosis:

– 50% had lesions confined to the outer serosal surface

– 37% had penetrated into the muscularis layer

– Only 10.5% had reached the submucosal layer

– And only 2.6% — 2 out of 76 women — had reached the mucosa that colonoscopy can see

The result: colonoscopy missed 92.1% of all surgically confirmed bowel endometriosis cases. Its sensitivity was 7 percent. Its negative predictive value was only 58 percent — meaning a negative colonoscopy provides almost no reassurance. The study authors concluded directly: “colonoscopy should not be routinely performed in the diagnostic work-up of bowel endometriosis.” [^1]

What A Gastroenterologist Can — And Cannot — Do For You

A GI evaluation is valuable for ruling out conditions that require their own treatment and that can genuinely coexist with endometriosis:

– Irritable bowel syndrome (IBS) — the most common misdiagnosis

– Inflammatory bowel disease (IBD) — Crohn’s disease and ulcerative colitis can involve the rectosigmoid and cause overlapping symptoms

– Colorectal polyps and colorectal cancer — must be excluded in women over 40 or with a family history who present with rectal bleeding

– Microscopic colitis — a mucosal inflammatory condition causing chronic watery diarrhea

– Celiac disease — malabsorptive disorder producing bloating, diarrhea, and fatigue that closely mimics endometriosis symptoms

– Appendiceal pathology — endometriosis of the appendix can cause recurrent right lower quadrant pain; concurrent appendiceal pathology needs exclusion

For any of these specific diagnoses, a gastroenterology evaluation is appropriate. Ruling out a concurrent or alternative diagnosis is a legitimate reason to see a gastroenterologist.

What a gastroenterologist cannot do is diagnose bowel endometriosis. The tools of gastroenterology — endoscopy, colonoscopy, mucosal biopsy — look at the wrong surface. A GI specialist who performs a colonoscopy and finds nothing has not excluded bowel endometriosis. A GI specialist who tells you “your colonoscopy was normal so your bowel symptoms are not structural” has provided a false reassurance.

Some gastroenterologists now advertise a “special interest” in endometriosis. Raising awareness that endometriosis can cause bowel symptoms — so patients get referred appropriately — is genuinely valuable. But the diagnosis of bowel endometriosis requires imaging, and the treatment requires surgery by gynecologic and colorectal specialists with specific expertise. A year on a GI waitlist is a year without a diagnosis.

The correct pathway runs through a gynecologist or reproductive surgeon who specializes in deep infiltrating endometriosis — not through gastroenterology. If a GI evaluation is needed to rule out something concurrent, the endometriosis specialist can order it — but it should not be the first stop.

The IBS Overlap: Why This Misdiagnosis Is So Common And So Costly

The symptoms genuinely overlap. A 2020 meta-analysis (Chiaffarino et al., Archives of Gynecology and Obstetrics) found that women with endometriosis were more than three times as likely to carry a concurrent IBS diagnosis as women without endometriosis. [^2] A 2025 US national database study found that women diagnosed with IBS were more than five times as likely to have a concurrent endometriosis diagnosis. [^3]

The distinguishing feature is cycle timing. IBS does not reliably worsen premenstrually and improve between periods. Endometriosis does. If the bowel symptoms follow the menstrual cycle, the diagnosis to pursue is endometriosis — until imaging proves otherwise.

SIBO:  A Real, Treatable Co-Condition

Not all gut symptoms in women with endometriosis are caused by endometriosis lesions directly. A growing body of evidence suggests that many women with endometriosis also have SIBO — small intestinal bacterial overgrowth — an excess of bacteria in the small intestine that causes bloating, gas, abdominal distension, diarrhea, and sometimes constipation.

SIBO occurs when bacteria that normally reside in the colon proliferate in the small intestine, where they ferment carbohydrates and produce gas (primarily hydrogen or methane). The result is significant bloating — often the diffuse, persistent kind that occurs outside menstruation, not just cyclically — along with urgency and irregular stool consistency.

A 2025 case-control study (Halfon et al., International Journal of Gynaecology and Obstetrics) confirmed substantially elevated SIBO and intestinal methanogen overgrowth (IMO) prevalence in women with endometriosis compared to controls. [^4] The plausible mechanisms include: endometriosis-driven inflammation altering gut motility; adhesions creating areas of intestinal stasis; and hormonal disruption of the gut microbiome.

SIBO matters because it is diagnosable and treatable. The test is a hydrogen/methane breath test — a simple, non-invasive outpatient procedure. Importantly, methane-producing organisms (IMO) do not produce hydrogen, so tests measuring only hydrogen will miss a significant proportion of cases. The best protocols measure both gases simultaneously.

Treatment typically involves a course of rifaximin — a non-absorbable antibiotic acting locally in the intestinal lumen with minimal systemic effects. Methane-predominant cases often require rifaximin plus neomycin. Treating SIBO will not cure endometriosis, but it may meaningfully reduce the portion of gut symptoms driven by bacterial overgrowth, making it easier to understand what remains truly endometriosis-driven.

This is a legitimate reason to see a gastroenterologist: if you have endometriosis and experience significant non-cyclical bloating or persistent gut symptoms that don’t clearly follow your menstrual cycle, requesting a SIBO breath test is reasonable and clinically actionable.

What Imaging Actually Works

Transvaginal ultrasound (TVUS) by an examiner with specific expertise in deep infiltrating endometriosis is the first-line tool. In expert hands, sensitivity for rectosigmoid endometriosis exceeds 85 percent. A standard gynecological ultrasound by a general sonographer will not reliably detect deep bowel lesions.

MRI protocolled for pelvic endometriosis offers the most complete anatomical map: exact lesion location, depth of bowel wall invasion, urinary tract involvement, and concurrent adenomyosis. It is essential for surgical planning. Standard abdominal MRI is insufficient — the protocol must specifically target endometriosis.

Transrectal ultrasound provides additional information about depth of rectal wall invasion and degree of luminal narrowing.

MR colonography — a specialized MRI technique combining pelvic imaging with bowel preparation and contrast enhancement — further improves sensitivity and specificity for colorectal involvement at centers where it is available.

Colonoscopy’s role is narrow: rule out colorectal cancer or polyps in appropriate-age patients with rectal bleeding; rule out IBD when biopsies are needed; or rule out other mucosal conditions when clinically indicated. It should not be ordered as a primary diagnostic tool for suspected bowel endometriosis.

Living with Undiagnosed or Medically Managed Bowel Endometriosis

For women who are not currently candidates for surgery, or who are awaiting evaluation, the following strategies can meaningfully reduce symptom burden:

– Symptom and cycle tracking: noting which symptoms correlate with the menstrual cycle helps distinguish endometriosis-driven symptoms from other causes and provides important data for your specialist

– Dietary modification: a low-FODMAP diet (reducing fermentable carbohydrates) can reduce bloating and bowel irregularity in some patients; an anti-inflammatory diet rich in omega-3 fatty acids and antioxidants may reduce the inflammatory component of symptoms

– Hormonal suppression: oral contraceptives, progestins, or GnRH agonist/antagonist combinations suppress estrogen-driven disease activity and can substantially reduce cyclical symptoms — but do not destroy lesions or reverse anatomical changes, and symptoms return when treatment is stopped

– Pelvic floor physical therapy: many women with bowel endometriosis develop secondary pelvic floor muscle dysfunction from chronic pain and guarding; targeted physical therapy can meaningfully improve bowel and pelvic symptoms independent of the underlying disease

– Mental health support: chronic pelvic pain and gut dysfunction carry a significant psychological burden; anxiety and depression are common in this population, and psychological support is a legitimate and important component of comprehensive care

Frequently Asked Questions

1. Is bowel endometriosis the same as regular endometriosis?

Bowel endometriosis is a subtype — specifically the form in which endometriotic tissue has invaded the wall of the intestine. It represents the more severe end of the endometriosis spectrum and is categorized as deep infiltrating endometriosis (DIE).

2. Why do my bowel symptoms get worse during my period?

Endometriosis lesions are hormonally active. They respond to the same estrogen and progesterone fluctuations that drive the menstrual cycle. Premenstrually, rising estrogen causes lesions in the bowel wall to swell, inflame, and become more mechanically irritating — producing cyclical pain, cramping, and altered bowel habits.

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

No — and this is one of the most important misunderstandings in the diagnosis of this disease. Bowel endometriosis grows on the outer surface and into the wall of the intestine, not on the inner mucosal surface that a colonoscope sees. A 2015 prospective study found that colonoscopy missed 92 percent of surgically confirmed bowel endometriosis cases. A normal colonoscopy should prompt a referral for endometriosis-specific imaging, not a conclusion that everything is fine. [^1]

4. I’ve been told I have IBS. Could it actually be bowel endometriosis?

Possibly — and this is extremely common. The key distinguishing feature is timing: bowel endometriosis characteristically worsens during the premenstrual and menstrual phases. IBS does not follow a predictable menstrual pattern. If your bowel symptoms are significantly worse around your period, the IBS diagnosis should be questioned and an evaluation for endometriosis should be requested.

5. What is SIBO, and could I have it along with endometriosis?

SIBO (small intestinal bacterial overgrowth) is an excess of bacteria in the small intestine that causes bloating, gas, and bowel irregularity. Research published in 2025 confirms significantly elevated SIBO prevalence in women with endometriosis. It is diagnosed by a hydrogen/methane breath test and treated with targeted antibiotics. If you have non-cyclical bloating or persistent gut symptoms, asking about SIBO testing is reasonable.

6. Is there any reason for me to see a gastroenterologist?

Yes, but for specific reasons: ruling out IBD, colorectal cancer or polyps, celiac disease, microscopic colitis — or diagnosing and treating SIBO. What a gastroenterologist cannot do is diagnose bowel endometriosis. Your primary appointment should be with an endometriosis-specialist gynecologist.

7. What exams should I ask my doctor about?

A dedicated pelvic MRI protocolled for endometriosis, and/or a transvaginal ultrasound performed by an examiner experienced in deep infiltrating endometriosis. If SIBO is suspected, request a hydrogen/methane breath test. Colonoscopy is useful only if colorectal cancer, polyps, or IBD must be actively excluded.

8. Can bowel endometriosis be diagnosed without surgery?

Yes. High-quality TVUS and pelvic MRI, performed by clinicians experienced in endometriosis imaging, can diagnose bowel endometriosis with high accuracy. Surgery should not be required just to make the diagnosis.

9. How long does diagnosis usually take?

Studies consistently report a diagnostic delay of seven to ten years from first symptoms. This reflects widespread misattribution of symptoms to IBS and poor endometriosis awareness in primary care and general gynecology.

Sources We Used

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1. Milone M, Mollo A, Musella M, et al.

Role of colonoscopy in the diagnostic work-up of bowel endometriosis.

World Journal of Gastroenterology. 2015;21(16):4997–5001.

DOI: 10.3748/wjg.v21.i16.4997

(Prospective, 174 women; colonoscopy sensitivity: 7%; missed 92.1% of surgically confirmed cases. Conclusion: colonoscopy should not be routinely performed in the diagnostic work-up of bowel endometriosis.)

2. Chiaffarino F, Cipriani S, Ricci E, et al.

Endometriosis and irritable bowel syndrome: a systematic review and meta-analysis.

Archives of Gynecology and Obstetrics. 2021;303(1):17–25.

DOI: 10.1007/s00404-020-05797-8

(11 studies; OR for IBS in women with endometriosis: 3.26 [95% CI 1.97–5.39].)

3. Walton KG, McGonigle W, Shukla AP.

Symptom overlap between irritable bowel syndrome and gynecologic conditions: a missed diagnostic opportunity.

American Journal of Gastroenterology. 2025.

DOI: 10.14309/01.ajg.0001132260.99578.19

(US national database; OR for concurrent endometriosis in women with IBS: 5.30 [95% CI 4.94–5.68].)

4. Halfon P, Estrade JP, Pénaranda G, et al.

High prevalence of small intestinal bacterial overgrowth and intestinal methanogen overgrowth in endometriosis patients: a case-control study.

International Journal of Gynaecology and Obstetrics. 2025.

DOI: 10.1002/ijgo.70005

(Case-control study confirming significantly elevated SIBO and IMO prevalence in women with endometriosis vs. controls.)

5. Fiorillo M, Neri B, Mancone R, et al.

Inflammatory bowel disease and endometriosis: diagnosis and clinical characteristics.

Biomedicines. 2024;12(11):2521.

DOI: 10.3390/biomedicines12112521

(Review of IBD-endometriosis overlap, differential diagnosis strategies, and multidisciplinary management.)

6. DiVasta AD, Zimmerman LA, Vitonis AF, et al.

Overlap between irritable bowel syndrome diagnosis and endometriosis in adolescents.

Clinical Gastroenterology and Hepatology. 2021;19(3):528–535.

DOI: 10.1016/j.cgh.2020.03.014

(Longitudinal study; odds of IBS 5.26-fold higher in adolescents with endometriosis than without.)

This is Part 1 of a two-part series. Continue reading: Part 2 — Treating Bowel Endometriosis: Surgical Options, Fertility, and What to Expect.

This article is for general patient education and does not replace individualized medical advice.