Why Miscarriages Still Happen After Transferring a PGT-Normal Embryo?

When a euploid embryo fails to implant—or worse, results in a miscarriage, it is a devastating let down. It’s a reminder that, even with how far technology has come, the science is far from perfect. Failed transfers and pregnancy losses can still happen.

My name is Dr. Lucky Sekhon and as a reproductive endocrinologist, I’ve had to break this heart wrenching news to patients before, and it never gets easier. I still remember every single case of pregnancy loss after transferring a seemingly perfect embryo. When an embryo is chromosomally normal, it’s easy to assume it means a guaranteed healthy pregnancy—but that’s not always the case.

If you’ve gone through a similar experience, you might be asking: Why did this happen? What went wrong? And what can I do differently next time? While we may not always find an exact answer, there are key reasons why a miscarriage can still occur—even when the embryo is “normal.”

How Common Is Miscarriage After a Euploid Embryo Transfer?

One of the hardest aspects of pregnancy loss is how isolating it can feel, but the reality is that miscarriage is more common than many realize. While preimplantation genetic testing (PGT) significantly reduces the risk by ensuring only embryos with the correct number of chromosomes are transferred, it does not eliminate miscarriage entirely. The risk of miscarriage after transferring a euploid embryo is estimated to be around 10-15%, which is much lower than the 20-30% miscarriage rate seen in the general population, and even higher for those over 40. However, once a heartbeat is detected, the risk of miscarriage drops to less than 5%. While these numbers are reassuring, they also highlight an important truth: even with the best available technology and a seemingly perfect embryo, pregnancy is still a complex and delicate process.

Why Does Miscarriage Happen After a Euploid Embryo Transfer?

A euploid embryo is the best possible starting point for a successful pregnancy, but several factors beyond the embryo itself can contribute to miscarriage.

1. Embryo Quality Is More Than Just Chromosomes

One of the biggest misconceptions about PGT is that it guarantees a “perfect” embryo. While it dramatically improves the odds, PGT only tells us that an embryo has the correct number of chromosomes—it doesn’t tell us everything about the embryo’s health or developmental potential.

• Mosaicism: PGT testing samples just a small portion (5-10 cells) from a 200-300 cell blastocyst. Some embryos contain a mix of normal and abnormal cells that may not be detected in the biopsy.
• Structural abnormalities: PGT doesn’t detect small deletions or duplications in the DNA that could impact fetal development. The purpose of PGT is simply to ensure the right number of chromosomes are present, it offers no visibility into the condition or quality of those chromosomes.
• Gene expression issues: Even if an embryo has the right number of chromosomes, the way its genes are turned on or off can still lead to developmental interruptions.

Pregnancy is an incredibly complex process. Having a euploid embryo is a huge advantage, but it does not guarantee implantation or full-term success.

2. Back To The Basics: The Reproductive Tract (Uterus + Tubes) Matters!!

Even the healthiest embryo needs the right conditions to thrive, and the uterus plays a critical role in implantation and sustaining a pregnancy. If the uterine environment is not optimal, even a euploid embryo may struggle to implant or progress. Factors such as a thin endometrial lining, fibroids, polyps, or scar tissue, and chronic endometritis (low-grade inflammation or infection in the uterine lining) can interfere with implantation. Additionally, autoimmune conditions may impact how the body interacts with the developing pregnancy. Before moving forward with another transfer, it’s important to assess the uterine environment through imaging, such as a saline sonogram or hysteroscopy, and address any underlying issues to create the best possible foundation for implantation. The role of chronic endometritis (inflammation/infection) in the lining in implantation failure or miscarriage is controversial—but in the case of unexplained euploid embryos not implanting or resulting in miscarriage, I tend to have a low threshold to do an endometrial biopsy, either alongside a saline sonogram or hysterosalpingogram (HSG) for repeat imaging of the uterus or at time of hysteroscopy, if a direct visualization of the uterine cavity or removal of polyps/fibroids/scarring is warranted. If chronic inflammation is identified on a biopsy, antibiotic treatment can be considered.

If there have been issues with thin lining, it may make sense to change the protocol used to prepare for a frozen embryo transfer (FET), or to consider alternative forms of estrogen if doing a medicated FET (I think vaginal estrogen in addition to oral estrogen tends to work well for thin lining, as it provides support for the lining, locally). Although the evidence may not be robust, I may also use vaginal viagra, baby aspirin, and supplements such as vitamin E and pentoxifylline in an effort to improve blood flow and drug delivery to the lining. When it comes to embryo transfer protocols: medicated vs. cryonatural— the data, and my clinical experience, suggests outcomes are similar, but it is never wrong to switch from one approach to another, if it medically makes sense, to see if your lining behaves better during natural ovulation versus with the support of estrogen.

If a HSG has never been done previously (because there was no medical history to suspect tubal disease such as endometriosis or prior STIs/ruptured appendix/multiple abdominal or pelvic surgeries), doing a HSG or HyCoSy (ultrasound that allows for tubal evaluation) to rule out a subtle hydrosalpinx that has evaded detection on standard pelvic ultrasound is key. I cannot tell you the number of patients who have come to me for second opinion after multiple failed transfers or euploid losses only to find out that they did in fact have a dilated or swollen tube all along, that was never checked. This is a simple, very obvious cause of failed transfer and early miscarriage, as the toxic fluid building up in blocked or damaged tubes directly communicate with the uterus and are toxic to embryos. If damaged, dilated tubes are identified, they must be removed before trying again, to reduce the future risk of miscarriage, ectopic, and failed transfers.

3. Placental Development Is Key

The placenta is the pregnancy’s lifeline, responsible for delivering oxygen and nutrients to the developing fetus. It begins forming between 7-10 weeks, and issues during this critical period can lead to early pregnancy loss. One key factor is poor vascularization, where the embryo does not establish strong enough blood flow connections with the uterine lining to sustain the pregnancy. Additionally, some embryos may develop normally at first but later fail due to placental abnormalities, that are not be detectable on PGT testing. This is why some pregnancies progress with normal beta hCG levels and even a detected heartbeat, only to result in an unexpected loss in the second half of the first trimester. When a miscarriage occurs after seeing a heartbeat, early placental dysfunction might be a contributing factor.

4. Getting Control of Underlying Maternal Health Conditions

Even when an embryo is chromosomally normal, certain maternal health conditions can impact pregnancy success. Blood clotting disorders like antiphospholipid syndrome (APLS) can increase the risk of miscarriage by affecting placental blood flow, which is why APLS testing is often considered after a euploid pregnancy loss and is part of the recommended work up for recurrent pregnancy loss. Uncontrolled thyroid disease, including hypothyroidism and Hashimoto’s, can also interfere with pregnancy, while diabetes and insulin resistance can negatively affect implantation and fetal development. Additionally, obesity (BMI >40) has been associated with higher miscarriage rates due to increased inflammation and hormonal imbalances. A thorough evaluation of maternal health before the next transfer can help identify any modifiable risk factors and optimize conditions for a successful pregnancy. Your medical history matters. I once had a patient with chronic asthma and a history of 2 unexplained failed euploid embryo transfers who had chronically elevated eosinophils on her complete blood count – something many patients with chronic asthma, which can have an autoimmune basis, can have. We decided to use a targeted treatment to suppress her eosinophil levels and she worked with her pulmonologist to get her asthma more under control and lo’ and behold— her next transfer worked and she now has a healthy baby girl. Getting any and all chronic medical conditions under control is of utmost importance. Uncontrolled disease, no matter what organ system it involves, can impact your overall fertility.

What This Means for Your Next Embryo Transfer?

If you are reading this, you might be preparing for an embryo transfer and feeling anxious about the possibility of miscarriage—even when transferring a PGT-tested embryo. That fear is completely understandable. There is so much at stake, and after all the time, effort, and emotion poured into this process, the idea of loss can feel overwhelming.

The good news is that PGT dramatically improves success rates and lowers the risk of miscarriage. By ensuring that an embryo has the correct number of chromosomes, PGT eliminates the most common cause of pregnancy loss. This is why miscarriage rates after a euploid embryo transfer are significantly lower—about 10-15%, compared to 20-30% in the general population. Once a heartbeat is detected, the risk drops even further, to less than 5%. These numbers mean that the vast majority of euploid transfers will result in a successful pregnancy.

However, it’s also important to have realistic expectations. PGT is a powerful tool, but it does not guarantee success because it only screens for chromosomal abnormalities. Other factors—such as uterine environment, placental development, and maternal health conditions—can still influence the outcome. This is why fertility specialists, like myself, take a comprehensive approach to evaluating and preparing for embryo transfer, ensuring that everything from endometrial health to hormone levels to underlying medical conditions is optimized before moving forward.

Trust the process. By transferring a euploid embryo, working with an experienced fertility team, and optimizing your health, you are taking every step possible to ensure a successful pregnancy. The data is on your side, and the chances of a positive outcome are overwhelmingly in your favor.

My name is Dr. Lucky Sekhon and I am the author of the Lucky Egg and a practicing REI based in New York City. I regularly publish content on fertility and reproductive issues on my Instagram and on this site. If you’d like to stay up to date with my latest content, I encourage you to subscribe to my free monthly newsletter. If you are interested in booking a consult with me at my NY office, you can submit a request here.