Endometriosis Root Causes According to Functional Medicine

Functional medicine views endometriosis not as a purely gynecologic condition, but as a whole-system inflammatory and immune dysregulation disorder with hormonal, gut, and environmental components.

Here’s a structured breakdown of the root-cause model used in functional and integrative medicine:

Inflammatory & Immune Dysregulation (The Core Driver)

Endometriosis is fundamentally an inflammatory, estrogen-responsive immune disorder — not just “misplaced uterine tissue.”

Mechanisms

• Immune dysfunction allows endometrial-like cells that reflux during menstruation to implant and persist instead of being cleared.

• Elevated macrophage and cytokine activity (IL-1β, IL-6, TNF-α, COX-2, prostaglandins) sustain chronic inflammation.

• Autoimmune overlap: higher rates of Hashimoto’s, celiac, and inflammatory bowel disease suggest loss of immune tolerance.

Functional Medicine Interventions

• Identify inflammatory triggers (food sensitivities, infections, toxicants, stress).

• Use anti-inflammatory nutrition (omega-3s, curcumin, resveratrol, sulforaphane).

• Support immune regulation (vitamin D optimization, gut-immune balance, adequate omega-3 index).

Estrogen Dominance / Detoxification Imbalance

Endometriotic tissue thrives in an estrogen-rich, progesterone-resistant environment.

Mechanisms

• Impaired phase I (CYP1A1, 1B1) and phase II (COMT, glucuronidation) detox pathways in the liver.

• Dysbiosis of the estrobolome (gut bacteria that recycle estrogens).

• Environmental xenoestrogens (plastics, pesticides, personal-care products).

Functional Medicine Interventions

• Support estrogen metabolism with DIM, indole-3-carbinol, calcium D-glucarate, sulforaphane.

• Optimize methylation: B12, folate, choline, magnesium, SAMe.

• Support bowel regularity & microbiome diversity (fiber ≥ 25–30 g/day, probiotics).

• Reduce xenoestrogen load (BPA-free, clean beauty, organic food).

Gut–Microbiome Axis & “Leaky Gut”

70%+ of immune cells reside in the gut. Dysbiosis increases systemic inflammation and alters estrogen recirculation.

Mechanisms

• Overgrowth of gram-negative bacteria → endotoxins (LPS) activate macrophages & prostaglandin release.

• Intestinal permeability → immune activation → cross-reactivity with endometrial tissue.Yeast overgrowth, SIBO, or low bile flow further promote estrogen recirculation.

Interventions

• Comprehensive stool or OAT testing for dysbiosis or fungal overgrowth.

• Targeted antimicrobials or probiotics (L. gasseri, L. reuteri, Bifido longum).

• Gu-repair nutrients: glutamine, zinc-carnosine, omega-3s, polyphenols.

Mitochondrial Dysfunction & Oxidative Stress

Endometrial lesions produce reactive oxygen species, perpetuating inflammation and pain.

Mechanisms

• Low glutathione, CoQ10, and poor mitochondrial respiration worsen fatigue & pain signaling.High oxidative stress damages surrounding tissues, further fueling cytokine release.

Interventions

• Mitochondrial nutrients: CoQ10, NAC, alpha-lipoic acid, carnitine, resveratrol.Increase antioxidant foods (berries, greens, spices).Address chronic toxin exposures (heavy metals, solvents, mold).

Detoxification & Environmental Toxicant Burden

Many women with endometriosis have higher tissue levels of dioxins, PCBs, phthalates, and BPA.

Mechanisms

• Dioxins stimulate endometrial proliferation and impair NK-cell cytotoxicity.

• Endocrine disruptors mimic estrogen, worsening hormonal imbalance.

Interventions

• Low-tox lifestyle (glass/stainless, filter water, air purifier, organic diet).

• Sweat therapy, sauna, fiber, and binders (chlorella, charcoal, modified citrus pectin) as appropriate.

Neuroendocrine & Stress Axis (HPA Dysregulation)

Chronic pain and trauma dysregulate cortisol rhythms, increasing inflammation and estrogen dominance.

Mechanisms

• High cortisol → progesterone shunting → worsened estrogen dominance.

• Stress-induced gut permeability & immune activation.

Interventions

• Cortisol assessment (AM/PM or DUTCH rhythm).Adaptogens (ashwagandha, rhodiola, holy basil — depending on cortisol pattern).

• Somatic therapies, meditation, breathwork, trauma-informed care.

Nutrient Deficiencies Common in Endometriosis

Nutrient	Role
Magnesium	Smooth-muscle relaxation, prostaglandin balance
Zinc	Immune modulation, tissue repair
Vitamin D	Anti-inflammatory, immune tolerance
B-vitamins	Methylation & detox
Omega-3 fatty acids	Down-regulate COX-2 and prostaglandins

Emerging Contributors

• Microbiome of the reproductive tract: altered vaginal and endometrial microbial balance.

• Stem cell theory: displaced progenitor cells responding to inflammatory cytokines.

• Epigenetic modulation: gene expression altered by diet, toxins, and stress.

 Putting It Together — Functional Medicine Framework

1. Identify triggers: infections, toxins, food intolerances, dysbiosis.

2. Calm inflammation: anti-inflammatory diet, omega-3s, curcumin, antioxidants.

3. Balance hormones: optimize estrogen detox and progesterone support.

4. Support detox & gut integrity: fiber, probiotics, liver nutrients.

5. Repair mitochondrial function: CoQ10, NAC, resveratrol.

6. Regulate stress & nervous system: adaptogens, breathwork, trauma-release practices.

7. Track biomarkers: hs-CRP, estradiol/progesterone ratio, ferritin, vitamin D, omega-3 index, gut testing.