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Here is a finding that runs against the grain of a lot of what you have probably read online: endometriosis comes bundled with a long list of other health conditions, but the vaginal microbiome does not appear to be the thing driving it.
When researchers actually look at the bacteria living in the vagina of people with endometriosis, they keep failing to find the dramatic, consistent shift you see in something like bacterial vaginosis.
This matters because the internet loves a tidy story, and ‘your vaginal bacteria cause your endometriosis’ fits the bill. The real picture, drawn largely from big citizen-science cohorts where thousands of participants self-sample at home, is more honest and more interesting.1
What did the citizen-science research actually find?
Citizen-science microbiome projects work by recruiting huge numbers of everyday people, in this case women and people with vaginas, to swab themselves at home and fill in detailed health questionnaires. The largest of these, the Isala project in Belgium, mapped the vaginal microbiomes of 3,345 participants and linked them to hundreds of life, health and lifestyle factors.1
The headline pattern from this kind of work is twofold.
First, endometriosis genuinely travels with other conditions. Second, when you compare the vaginal bacterial communities of people with and without endometriosis, the difference is far smaller and far less consistent than the dysbiosis story suggests.
Endometriosis really does come with comorbidities
This part of the science is solid. Endometriosis is increasingly understood as a whole-body, inflammatory condition rather than a problem confined to the pelvis.2
A large data-driven study of more than 8,000 women with endometriosis, matched against controls, confirmed the conditions clinicians already suspected and turned up some new ones.2
Conditions more common in people with endometriosis include:
- Migraines and other headache disorders
- Allergic conditions, including allergic rhinitis
- Fibromyalgia and chronic pain syndromes
- Gastro-oesophageal reflux and gut symptoms
- Sinusitis, and even some unexpected ones like sciatica
Autoimmune conditions also cluster with endometriosis at higher-than-expected rates, which fits the idea of a body-wide inflammatory and immune component.3
The takeaway here is not that endometriosis causes all of these directly. It is that they share underlying biology, including inflammation, immune dysregulation, chronic pain processing and hormonal signalling, so they tend to show up together.2
So where does the vaginal microbiome fit in?
This is where the story gets more nuanced. You would expect, given how often the vaginal microbiome is blamed, that those with endometriosis would have an obviously disrupted community, low in protective bacteria and high in disruptive ones. The evidence does not support a clean version of that.4
When researchers measure the overall diversity and makeup of the vaginal microbiome, people with endometriosis often look much like everyone else. Several studies find no significant difference in bacterial diversity between endometriosis and controls, and the few signals that do appear are inconsistent from study to study.4
In other words, there is no reliable ‘endometriosis microbiome signature’ the way there is for bacterial vaginosis (BV), where protective Lactobacillus species are clearly displaced by a mixed community of disruptive bacteria.4
Why this is different from BV
BV is the textbook example of vaginal dysbiosis. The protective bacteria drop away, the pH rises, disruptive bacteria and biofilms take over, and you can measure that shift consistently across populations.
And, in My Vagina’s specialist clinic, we have found that BV is often the end result of another process in the body not working well, like whatever also causes endometriosis, resulting in disruption to the vaginal ecosystem. BV, and other forms of vaginal dysbiosis, can be the result of a health condition, not the cause of it.
The vaginal microbiomes of those with endometriosis are not behaving in a consistent manner. The pooled data hint at a slightly higher chance of vaginal dysbiosis in some with endometriosis, but it is a weak, inconsistent association, not a strong, repeatable pattern.4
That distinction is the whole point. A weak, on-again-off-again association is not the same as a cause.
What this means for you
If you have endometriosis, this is genuinely reassuring news, not a dead end.
It means you do not need to blame yourself or your vaginal bacteria for a condition that is rooted in inflammation, immunity and hormones across your whole body. The microbiome is one piece of a much bigger puzzle, not the master switch.4
It also means that looking after your vaginal microbiome remains worthwhile in its own right, for comfort, for protection against infections, and for general gynaecological health, even though it is not a proven lever for endometriosis itself. Supporting your protective bacteria (if they are at risk due to heavy inflammation) with targeted probiotics and a Lactobacillus-friendly routine is sensible preventative vaginal care.
Frequently asked questions
Does endometriosis change your vaginal microbiome?
Not in a clear, consistent way. Some studies find small differences, others find none, and there is no reliable endometriosis-specific microbiome signature. This is very different from BV, where the disruption is obvious and repeatable.4
If the microbiome is not the cause, what is?
Endometriosis is driven by a mix of inflammation, immune dysregulation, hormonal signalling and genetics, acting across the whole body rather than just the pelvis. That is why it travels with so many other conditions.2
What comorbidities are linked to endometriosis?
Common companions include migraines, allergies, fibromyalgia, reflux and gut symptoms, sinusitis, and autoimmune conditions. These share inflammatory and immune biology with endometriosis.2,3
Should I still look after my vaginal microbiome?
There is no need to treat if your microbiome looks healthy and you don’t have any symptoms. But, if you’re prone to imbalances and infections, preventative measures can protect you.
Why do so many articles say the microbiome causes endometriosis?
Because association studies can find small differences, and those get reported as if they were causes. Large, careful cohorts and meta-analyses paint a more cautious picture: real comorbidities, but no proven microbiome shift driving the disease.4
What to do next
If you are living with endometriosis, the most useful moves are the ones that address the whole-body picture: working with a clinician on pain and inflammation, and keeping your intimate health in good shape alongside that.
If you want to know where your own vaginal bacteria stand, a microbiome test can map your protective and disruptive species, and our team can help you make sense of the results. Supporting protective bacteria with a quality vaginal probiotic is a reasonable, low-risk part of your routine.
Have a question about endometriosis, your microbiome, or your symptoms? Aunt Vadge’s Assistant is in the bottom left of your screen, ready to chat right now, and if you’re not sure, our practitioners can help you build a plan that treats you as a whole person, not a single swab.
Related Posts
References
- Lebeer S, Ahannach S, Gehrmann T, et al. A citizen-science-enabled catalogue of the vaginal microbiome and associated factors. Nature Microbiology. 2023;8(11):2183–2195. Full text
- Zelovich T, Erenberg M, Klaitman-Mayer V, et al. Unveiling endometriosis hidden comorbidities using a data-driven approach: a retrospective matched cohort study. npj Women’s Health. 2025;3:30. Full text
- Aziz M, Beaton MA, Aziz MA, et al. Endometriosis and autoimmunity: a large-scale case-control study of endometriosis and 10 distinct autoimmune diseases. npj Women’s Health. 2025. Full text
- Qing X, Xie M, Liu P, et al. Correlation between dysbiosis of vaginal microecology and endometriosis: a systematic review and meta-analysis. PLOS ONE. 2024;19(7):e0306780. Full text
