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Bowel Endometriosis Symptoms: A Natural Treatment Guide

Written by Dr. Michael Ruscio, DC on September 9, 2025

Written by Dr. Michael Ruscio, DC on September 9, 2025 — Reviewed by Hilary Watts

• Symptoms|
• What It Is|
• The IBS Connection|
• Diagnosing & Conventional Treatments|
• Natural Treatment Guide|

These and other symptoms can be managed with natural treatments like an anti-inflammatory diet, probiotics, and lifestyle strategies.

For many women, bowel endometriosis goes overlooked for years. Many of the symptoms, like diarrhea, constipation, bloating, abdominal pain, and painful bowel movements, often get lumped together with irritable bowel syndrome (IBS) or another gut issue. And if you typically struggle with painful periods, nausea, or vomiting—symptoms that overlap with bowel endometriosis—it’s easy to feel unheard and without answers.

If this sounds familiar, you’re not alone. Understanding the full picture of bowel endometriosis symptoms is the first step toward clarity. From there, you can better evaluate your options—whether that means conventional treatments or natural approaches, like an anti-inflammatory diet and probiotics that may offer real relief.

What Are the Symptoms of Bowel Endometriosis?

Bowel endometriosis symptoms are often non-specific and can mimic those of other digestive disorders like IBS and inflammatory bowel disease (IBD), making diagnosis difficult. Some women may have no symptoms at all, but others can experience 1 2 3:

• Diarrhea
• Constipation
• Painful bowel movements
• Small bowel obstructions (this is rare)
• Painful periods
• Pain during sexual intercourse
• Chronic abdominal pain
• Blood in the stool
• Bloating
• Pain while sitting
• Radiation of pain to the perineum (the area between the anus and vagina)
• Mucus in the stool
• Rectal bleeding
• Nausea
• Vomiting
• Pain in the rectum

What Is Bowel Endometriosis?

To better understand bowel endometriosis, let’s review endometriosis. Possibly affecting about 10–15% of menstruating people, this chronic, inflammatory disease occurs when tissue resembling the innermost lining of the uterus (endometrium) implants itself outside the uterus 4. Although the most common location for this is in the ovaries, endometrial tissue can also find its way to the GI tract.

The specific cause of endometriosis is unknown, but it probably occurs from a combination of 4:

• Inflammation
• Oxidative stress from too many free radicals (reactive atoms that can damage cells, proteins, and DNA) and not enough antioxidants
• Hormonal disturbances (high estrogen and/or low progesterone)
• Genetics 
• Epigenetics (changes in which genes are expressed)
• Environment

Diagnosing endometriosis can be tricky and take many years 4. The gold standard is visual laparoscopic inspection by a surgeon or surgical gynecologist to look for lesions or growths.

When endometrial-like tissue infiltrates the GI tract, it’s referred to as bowel endometriosis. This is the most common type of endometriosis that occurs outside the pelvis—it can affect up to 37% of women with endometriosis 2.

Bowel endometriosis manifests as deep or shallow lesions (clumps of endometrial-like tissue) in the wall of the small bowel and/or large bowel—most commonly the rectum and sigmoid colon 1. Lesions that are larger and deeper are also called nodules. Women with deeper bowel wall lesions often have more severe symptoms and lesions that are less likely to go away 2.

Conventional Treatment

Conventional medical advice can include a variety of pharmaceuticals like oral birth control pills, non-steroidal anti-inflammatory drugs (NSAIDS like ibuprofen), and progestins (hormone replacement). For more severe cases, treatments may include laparoscopy to remove endometrial tissue or even surgery to remove part of the bowel.

The Bowel Endometriosis–IBS Connection

There’s a strong connection between gut health and endometriosis.

The lesions that form in the intestines from bowel endometriosis damage the tissue there, including certain gut cells and the gut’s nervous system. 

When damage occurs in these areas, it can change the gut’s motility (how fast food moves through) and increase gut sensitivity.  

Not only that, but if you are taking medication like opioids or GnRH to help with endometriosis, you might experience gut-related side effects, like constipation 2 5.

Women with endometriosis can have up to a three-fold increased risk for IBS 6, which shares similar problems to endometriosis, such as 7:

• Chronic inflammation
• Increased feelings of pain 
• Mast cell activation syndrome (when your immune system is in overdrive)
• Gut bacteria imbalance (which can disturb estrogen levels) 8
• Leaky gut

People with bowel endometriosis can experience the following IBS- and IBD-like symptoms, which may relate to the size of endometriosis bowel nodules (larger nodules cause more symptoms) 3 9:

• Diarrhea
• Constipation
• Abdominal pain
• Bloating
• Painful bowel movements
• Mucus in the stool
• Rectal bleeding that comes and goes

Bowel movements often relieve many of those symptoms in people with only IBS, but that doesn’t seem to be the case for those with bowel endometriosis 9.

Diagnosis & Conventional Treatments for Bowel Endometriosis

Bowel endometriosis can mimic IBS or other gut issues, making it difficult to diagnose without specialized evaluation. 

Clinical Diagnosis & Imaging

• Medical history: Describing your experience can reveal symptoms that suggest bowel endometriosis 10.
• Physical exam: A pelvic exam of both the vagina and rectum, ideally during menstruation, may detect areas of tenderness that suggest bowel involvement 10.
• Imaging tests like transvaginal ultrasound and possibly MRI can help identify lesions and rule out other issues 10.
• Laparoscopic excision surgery: In some cases, this minimally invasive surgery to cut out disease is the only way to confirm a diagnosis—but it’s invasive and typically reserved for more severe or persistent cases 1.

Conventional Treatment

• Medical management: Uses hormones to slow disease and ease symptoms; can be used before or after surgery, but may only work temporarily 10.
• Hormonal treatments (general): Long-term hormone suppression (often birth control pills or progestins) to control symptoms with fewer side effects 10.
• Progesterone therapy: Progestins (like norethindrone) can reduce pain, diarrhea, cramps, and rectal bleeding, though some women still need surgery later 10.
• GnRH agonists (e.g., leuprolide): Strong hormone blockers that shrink disease and relieve symptoms, but side effects (like hot flashes) limit their long-term use 10.
• Other options: Devices like the hormonal IUD or drugs like intravaginal danazol may reduce pain, but evidence is limited and based on small studies 10.
• Surgical management: Removal of diseased tissue through minimally invasive surgery, usually done only for women with severe or lingering symptoms and by a team of skilled gynecologic and gastrointestinal surgeons 10. Although medications and surgery are sometimes necessary, they are not the only paths to relief. Many women see significant improvements in bowel-related endometriosis symptoms by addressing underlying inflammation, hormone imbalances, and gut health. 

In the next section, we’ll explore natural treatment strategies that may help you manage symptoms and avoid medications and surgery altogether.

Natural Treatment Guide For Bowel Endometriosis Symptoms

Women with endometriosis have at least twice the risk of IBS compared with those without, even if they don’t have a diagnosis of bowel endometriosis 6 11. This overlap in symptoms means we can implement some of the same treatment strategies we use for IBS to target bowel endometriosis symptoms.

Diets For Bowel Endometriosis Symptoms

Current research on diet and bowel endometriosis is limited, but several diets have the potential to improve endometriosis symptoms. 

A meta-analysis looked at 11 randomized controlled trials testing diet or supplements for endometriosis. Some studies suggested that antioxidant supplements and a nutrient-dense diet may help with pain during the period, but stronger, higher-quality studies are needed 12.

Nutrient-dense dietary patterns that may help bowel endometriosis symptoms are 13:

• Mediterranean diet
• Gluten-free diet
• Low nickel diet
• Elimination diet (such as low FODMAP) 14

One study found that women with both IBS and endometriosis who tried a low FODMAP diet—a short-term diet that limits bacteria-feeding carbs—for four weeks were about three times more likely to see major improvements in bowel symptoms than women with IBS alone 14.

A trial of a nutritious low FODMAP diet may improve your symptoms, especially if you also have IBS. If you’d like to try a low FODMAP diet, my free Low FODMAP Diet Guide can walk you through it. 

The low FODMAP diet is an effective place to start, but if it feels intimidating or too restrictive to try right now, another great elimination diet is a Paleo diet, which removes many common food allergens and inflammatory foods. Paleo is a well-rounded option that also helps to regulate blood sugar and promote hormone balance. 

If you’re interested in trying a Paleo diet but don’t know where to start, download my Paleo Diet Guide, a printable handout that simplifies the diet. 

Lifestyle Strategies for Bowel Endometriosis Symptoms

While you’re working on finding the right diet, consider lifestyle factors that may be contributing to your bowel endometriosis symptoms. Ask yourself if disrupted sleep, excess stress, and a lack of physical activity could be contributing to your symptoms. 

In the clinic, we have found that simple lifestyle tips can go a long way. Consider practicing the following three lifestyle habits and see how your symptoms improve. 

1. Make great quality sleep non-negotiable. Poor sleep can negatively affect gut function and may worsen symptoms of bowel endometriosis. Create a healthy sleep routine that works for you and stick with it.
2. Practice a daily stress-management technique. Unmanaged stress can also negatively impact your gut microbiota, leading to worse digestive symptoms. Deep breathing and meditation are both great options for relieving stress. One study found that women with endometriosis who performed Hatha yoga for eight weeks had better quality of life and less pain 15.
3. Move your body every day. A meta-analysis of six trials found that physical activity and exercise can improve quality of life, reduce pain, and support mental health and pelvic floor function for people with endometriosis 16. Exercise has plenty of health benefits, but it can also improve your gut microbiome diversity. Walking is the foundation of fitness, so if you’re new to exercise, you might add a 10–30-minute walk every day and branch out from there. Strength training and cardiovascular training may improve a variety of endometriosis symptoms, including those related to mental health.

If you’ve had some improvement with a healthier diet and lifestyle, but are still experiencing bowel endometriosis symptoms, you might consider supporting your gut health with probiotics.

Probiotics for Bowel Endometriosis Symptoms

There’s no human research evaluating probiotics for treating bowel endometriosis (yet), but we do know probiotics can improve a variety of gut-related conditions. 

As I discuss in my book Healthy Gut, Healthy You, probiotics have consistently shown to be an effective treatment for IBS, small intestinal bacterial overgrowth (SIBO), leaky gut, IBD, and celiac disease. 

When it comes to endometriosis, a few studies have examined the effects of probiotics:

• One randomized controlled trial found that six months of probiotics (in combination with a multivitamin/mineral supplement and fish oil) may have helped relieve endometriosis pain 17. 
• Two randomized controlled trials found that probiotics significantly decreased menstrual pain and overall endometriosis pain after 8–12 weeks 18 19.

Since probiotics are extremely safe, have been extensively studied, and provide benefits for a variety of gut conditions, it may be worth it to try this therapy. 

Other Complementary and Alternative Therapies for Bowel Endometriosis Symptoms

If you’ve worked through the above but still want additional options, manual physical therapy and/or acupuncture have both been shown to improve symptoms in women with endometriosis. For example:

• Physiotherapy: A meta-analysis found that physiotherapy approaches like electrotherapy and laser devices are effective at reducing pain in women with endometriosis 20.
• Acupuncture: A meta-analysis showed that hands-on acupuncture may improve endometriosis pain and quality of life 21.
• Manual physical therapy: Limited research suggests that bodywork approaches like the Wurn technique may help loosen scar tissue and improve soft tissue mobility in the abdomen and pelvic floor, reducing pain during sex and menstruation 22.

Simple Changes Can Soothe Bowel Endometriosis Symptoms

Bowel endometriosis can cause diarrhea, constipation, abdominal pain, bloating, nausea, painful periods, painful bowel movements, and blood in the stool. 

You can ease symptoms by following a nutrient-dense, anti-inflammatory diet, taking probiotics, and making targeted lifestyle changes. These steps may also help you manage or reduce medication and avoid surgery—but always check with your doctor before changing any prescriptions.

If you need help navigating gut-related symptoms or bowel endometriosis, we are now accepting new patients and would love to help. Book an appointment with us today.

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