Implantation failure and recurrent miscarriage

Chronic endometritis and dysbiosis treatment in Ireland

Medically reviewed by Dr. Phil Boyle, MICGP, MRCGP · Last reviewed July 2026

Chronic endometritis is a persistent inflammation of the uterine lining that can be due to pathogenic bacteria or a lack of healthy lactobacillus bacteria (dysbiosis). At NeoFertility, we investigate it as a treatable cause of infertility, implantation failure and recurrent miscarriage, because a healthy uterine environment is as important as a healthy egg.

Our preference is to send both menstrual and semen samples to test the microbiome and offer probiotic or antibiotic treatment as indicated. It is important to re-test after treatment to ensure optimal conditions have been achieved.

A treatable condition that standard workups miss

Chronic endometritis, or CE for short, is a low-grade persistent infection of the endometrium, the inner lining of the uterus.

It is not the same as acute pelvic inflammatory disease. It does not typically cause fever or severe pain. In many cases it causes no symptoms at all, or only very subtle ones: brown spotting between periods, light discharge, or a vague pelvic ache.

More fertility clinics are recommending this testing to improve outcomes, although more research and published studies are needed.

The endometrium is where implantation happens. When it is chronically inflamed, the tissue structure changes and the local immune environment shifts. The embryo finds a lining that is not receptive, increasing the risk of failed implantation or early pregnancy loss.

A healthy uterine environment is as important as a healthy egg.

Who tends to present with chronic endometritis

In Dr. Boyle's clinical experience, chronic endometritis shows up in a recognisable pattern.

It often appears in couples with unexplained impaired fertility who ovulate normally, have adequate hormone levels, and have no obvious structural problem, yet do not conceive. It is also common in women with recurrent miscarriage, especially early losses with no chromosomal cause identified.

It turns up, repeatedly, in women who have been through IVF cycles with good-quality embryos that simply did not implant. The consistent finding in clinical practice is that this condition is far more common than most standard workups would suggest.

If you have been told your investigation is "unexplained," it is worth asking whether the uterine lining was ever directly assessed. In a 187-couple cohort, unexplained infertility fell from 24% to 1% after a full NeoFertility workup (Boyle et al., JRRM 2025).

That shift happens because we look at things that are evolving, and the endometrial environment is one of them.

Investigating chronic endometritis

So what we do is look at the clinical picture first.

We look at the pattern of bleeding, any brown spotting, discharge between periods, or unexplained short luteal phases. Brown spotting, in particular, is a clinical sign that Dr. Boyle takes seriously as a possible indicator of uterine lining inflammation.

The most reliable way to confirm chronic endometritis or dysbiosis is to test a menstrual sample. A menstrual sample can be collected using a menstrual cup and sent for testing of the microbiome to see if probiotics or antibiotic treatment may be helpful.

Hysteroscopy, a thin camera passed through the cervix into the uterine cavity, and allows a biopsy to be taken at the same time. Where a biopsy result is unclear, microbiome testing of the lining can give a more detailed picture of the bacteria present.

In the restorative approach, diagnosis is not a single test but a clinical picture built from multiple data points. We look at the chart, we look at the hormones and we look at the lining.

When the clinical presentation points toward chronic endometritis, we investigate and treat it.

Treatment for chronic endometritis

Chronic endometritis is an infection, and the treatment is antibiotics.

The organisms most commonly involved include anaerobic bacteria, Ureaplasma, Mycoplasma, and Enterococcus, among others. No single antibiotic covers the full range, which is why a combination is typically used, depending on what is found.

In Dr. Boyle's clinical experience, suspected chronic endometritis is often best treated with combination antibiotics. An antifungal is sometimes added to protect against overgrowth during the course. This approach has evolved through a series of complex cases.

As of 2026, the preference is to guide the probiotic and antibiotic choice from microbiome testing of the lining. This is more precise than relying on a standard combination. The principle is the same as for any antibiotic: identify the target organism, then treat it precisely. Antibiotic treatment may be enhanced by treating with biofilm disruptors and probiotics.

After optimising the microbiome, the focus moves to supporting the full cycle. We monitor progesterone and oestradiol at 7 days post ovulation (7 DPO), we track follicle development, and we treat whatever hormonal imbalance remains.

In Dr. Boyle's clinical experience, many couples with long-standing unexplained impaired fertility can conceive after this kind of combined approach. Treatment includes cycle support, antibiotics for endometritis, and hormonal support through pregnancy.

Chronic endometritis, when found and treated, can remove a barrier that standard workups may miss.

Chronic endometritis alongside other reproductive health conditions

Chronic endometritis rarely sits on its own.

In practice, it often overlaps with other conditions: suboptimal ovulation, hormonal dysfunction, endometriosis, or immune dysregulation. The restorative approach does not treat one condition and assume the rest are fine. We look at the full picture.

If you have a history of endometriosis, the uterine lining environment is worth investigating on its own terms. The two conditions share some inflammatory mechanisms, but CE is a distinct diagnosis requiring its own treatment.

You can read about how NeoFertility approaches endometriosis at the endometriosis page.

For couples where recurrent miscarriage is the main concern alongside suspected CE, the recurrent miscarriage page covers the full workup we apply. If the broader picture points toward unexplained impaired fertility, the unexplained infertility page explains how we work through that category.

Getting started

The first appointment is a 45-minute consultation with Dr. Phil Boyle or Dr. Agnes Toth.

No GP referral is required. We ask that you begin charting with ChartNeo before your first appointment where possible. The cycle data you bring with you is part of the investigation from day one.

If you notice brown spotting, discharge between periods, or any pattern that does not match the standard cycle, document it in the chart.

A single IVF cycle in Ireland typically costs EUR 5,000 to EUR 8,000. Repeated IVF without investigating the uterine environment can mean cycle after cycle building on the same unresolved problem. The NeoFertility treatment plan is a fraction of that cost.

You can see full pricing at our pricing page.

If you are ready to take the next step, book your first consultation. If you would prefer to read more first, our three-phase treatment plan explains exactly how the restorative approach works from initial investigation through to pregnancy support.