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Recurring chemical pregnancies – when your body keeps saying no, time and time again

Updated: May 6, 2022

I didn’t even know what a chemical pregnancy was until I had suffered my first one in 2010, which was when my first son was around 18 months old. I had only just started trying to get pregnant again after giving birth to my son in 2008, so I wasn’t totally over the moon when I discovered my period was nearly a week late. I guess I didn’t quite feel ready to be pregnant again. After 5 days of getting used to the idea of being pregnant again, it was all over as I started bleeding. I was devastated.

It took this loss to realised that I was actually happy to be pregnant after all. I then went on a mission to get pregnant again as fast as I could. Unfortunately, it took another 10 long years, 17 chemical pregnancies, and 2 miscarriages later to realise my dream of having a sibling for my son.

Recurring chemical pregnancies can be a tough road as they occur so early on (between 4 – 5 weeks), so they are not technically referred to as normal miscarriages. As a result, you find it harder to seek help from your GP and fertility specialist. This is because by the time you have sought help you no longer have a positive pregnancy test or detectable HCG, so there is no actual evidence that you were pregnant. Whereas with a later miscarriage you have a record of the HCG tests that you get when you first go to the doctor, which is usually around the 5 week mark. With chemical pregnancies, It is all over so fast, before you have a chance to get any blood tests done.

The more chemical pregnancies I had, the more anxiety I faced towards the end of the two weeks wait. I just couldn’t bring myself to take a home pregnancy test until at least 5 weeks had passed. Many times, I didn’t take a test but I still knew, you just feel different, your body knows.

What are chemical pregnancies?

A chemical pregnancy is a very early miscarriage that occurs when an egg is fertilized but doesn’t fully implant in the uterus. The pregnancy is usually lost between 4 and 5 weeks. It is referred to as a `chemical pregnancy’ as you may have had an initial positive pregnancy test if you test early enough, but after a few days to a week later you start to bleed and subsequently have a negative pregnancy test as HCG levels drop off.

Chemical pregnancies are fairly common and if you weren’t trying to get pregnant, it would likely be a late period that is slightly heavier than normal and crampier so you may not even notice. When you are trying to get pregnant though, with a chemical pregnancy I did feel pregnant during those cycles, so you are more aware that it is happening and for me, because it occurred so often, I would feel very anxious and couldn’t bring myself to test until at least 5 weeks.

Although I lost count in the end I estimate that I had suffered about 17 chemical pregnancies over a 10-year period. I often went to the GP and fertility doctor to talk about my situation but I wasn’t really offered any support as technically they weren’t considered actual miscarriages, and I needed to have at least 3 actual miscarriages before I could be referred for further testing. I did later go on to have 2 later miscarriages (at 6.5 and 8 weeks) and had some investigative testing with my fertility clinic, but still, no reason was found and I was labeled as having `unexplained infertility'

So my mission was to try and understand, through my own research, why I kept having chemical pregnancies time and again, and after each one, I would try different approaches in terms of diet, lifestyle, and supplement.

Causes of chemical pregnancies

There are many causes of chemical pregnancies which I explored most of these with myself over the years, but nothing appeared to be obvious. Chemical pregnancies are usually a failure of the embryo to implant properly into the lining of the uterus. It is where an egg becomes fertilised but the implantation process is not completed. The common causes are:

  • Chromosomal abnormalities - around 50%

  • Uterine abnormalities e.g., fibroids, endometriosis

  • Gynecological Infections

  • Low thyroid function

  • Hormone imbalances such as luteal phase defect

  • Low body mass index

  • Smoking and excessive alcohol consumption

  • Autoimmune issues

After 10 years of going around and around on this chemical pregnancy roundabout, I was surprised when I conceived naturally at age 43 and went on to give birth with no complications to a healthy baby girl at age 44. I waited until 5.5 weeks to do a pregnancy test as I was waiting for the usual chemical pregnancy to occur before 5 weeks but amazingly it didn’t. So why after all this time did this pregnancy continue? This was purely a miracle. I have identified a couple of key reasons which I think may have contributed to it but I really don’t know for sure.

  1. Increased low vitamin B12 levels (methylation) – more on this shortly

  2. Optimised folate levels with just natural folate and no folic acid at all (methylation) – for many years I had made the mistake of taking a prenatal multivitamin with folic acid even though I was taking a separate methylfolate supplement. All folic acid needs to go in favour of methylfolate. See my previous blog here for more information.

  3. Optimised vitamin D levels – more on this shortly

  4. Balanced hormones - my cycles were pretty regular with no PMS, good energy levels, and mood. I had been supporting my progesterone levels for a while with the herb vitex and homeopathy. I also started taking the mineral Boron 3 months prior to conception as I thought I was experiencing perimenopause and according to kinesiology testing, I needed this. I have written another blog post about Boron and fertility over age 40 so you can check it out here.

  5. Lowered stress levels - I reduced my work hours which made space for a baby

  6. Immune regulation during the luteal phase – more on this shortly

Even though I had worked on these areas individually over the years, maybe finally everything was in balance and optimally aligned. Or maybe it was just my time. I like to believe this.

Vitamin B12

Vitamin B12 is a huge player with fertility and a deficiency in vitamin B12 is a major cause of recurring miscarriage, especially early pregnancy loss before 5 weeks. Yet it is rarely tested by general practitioners and fertility specialists. During my 10-year journey with secondary infertility and recurring pregnancy loss, my B12 was not tested at all. Yet vitamin B12 plays an important role in folate metabolism and we all know how important folate is.

It was only later on in my journey that I realised the significance of B12 and arranged to get myself tested. This was just after my IVF miscarriage as I felt at the time that my mind was foggy and I couldn’t concentrate on anything. It was no wonder my B12 (and Iron) was low after IVF as I had so much blood drawn for blood tests during that period. B12 proved to be one of the missing links with me, especially as it is linked in clinical studies to recurring early pregnancy loss before 5 weeks which is something I was struggling with. When I did eventually get pregnant 3 years later, I needed high doses of B12 in the form of methylcobalamin daily throughout my pregnancy.

Vitamin B12 is an essential nutrient. It works together with folate in the synthesis of DNA, RNA, and red blood cells. Adequate levels of B12 maximise the uptake of folate. Vitamin B12 also helps to regulate brain activity and is involved in the production of the myelin sheath around the nerves and the conduction of nerve impulses. It is also important for methylation, an important liver detoxification pathway, and reducing homocysteine levels. High levels of homocysteine levels in the blood can contribute to miscarriage and are caused by low levels of the methylation nutrients folate, B12 and B6. So, supplying these nutrients can help to bring homocysteine levels down.

In a female vitamin B12 also helps to boost the endometrium lining to prepare for implantation, which decreases the chances of complications. For more information on Vitamin B12 and recurring pregnancy loss check out my previous blog post here.

Connection with autoimmunity

I never really knew for certain why I kept having recurring chemical pregnancies, there was nothing conclusive that came out of any testing, however, I had a gut feeling that there was some immune issue going on which was affecting implantation, as this is the point where everything started to fail. I felt it was either an autoimmune issue or an increase in natural killer cells in the uterine lining that essentially attacked the embryo and interfered with implantation. The problem was there was no way of testing this, so I never really knew for sure.

Autoimmune conditions run in my family, my grandmother had autoimmune thyroid disease (as does my aunt), my dad has Rheumatoid Arthritis and I myself found out that I had Coeliac Disease in my early 30’s and have been strictly 100% gluten free ever since. I had been tested for antinuclear antibodies (ANA), lupus antibodies, and antiphospholipid antibodies a couple of times during my time with fertility associates but there were never any signs of elevated antibodies. This to me did not mean that there wasn’t an immune reaction going on somewhere as it is only a presentation of a large number of ANA antibodies that indicate an autoimmune attack is occurring in the cells of your body tissues. I felt that I had no problems conceiving but things started to go wrong at the implantation stage time and time again.

As I was already strictly 100% gluten free, and I would recommend this for anyone with fertility and recurring miscarriage issues, and I had been working on healing my gut for a long time with periods of time on and off the GAPS diet, I wondered what else I could do to support my body if there was some sort of immune attack going on. At the time my health and energy levels were really good and previous skin and asthma issues had pretty much cleared up. I didn’t really have any health issues to report other than fertility.

Supporting autoimmunity with nutrients

The key nutrients to make sure you are optimising if you have an autoimmune condition are vitamin D and Selenium which help to modulate the immune system, so I made sure I took these nutrients each day.

Vitamin D

Vitamin D can often be the missing link in cases of infertility. It is such an important vitamin because it has an effect on over 2,000 genes in the body.

Vitamin D3 (cholecalciferol) is known as the `sunshine vitamin’ because it is produced by the skin when it is exposed to the sun. If we spend enough time out in the sun on a daily basis, most of us could make enough vitamin D. However, many of us don’t get enough consistent sun exposure to maintain normal vitamin D levels throughout the year, with levels dropping for most people over the wintertime.

Vitamin D3 can also be found in foods such as eggs, cod liver oil, mushrooms, fatty fish such as tuna and salmon, and cow’s milk, but it can be difficult to get enough in the diet.

Vitamin D3 is considered to be a hormone rather than a nutrient. It helps the body create sex hormones such as progesterone and estrogen which in turn affects ovulation and healthy hormone balance.

A deficiency in vitamin D3 has been associated with various autoimmune conditions as it has a modulating effect on the immune system. As many fertility issues can be a result of an underlying autoimmune condition it is important to get vitamin D levels checked.

Taking vitamin D has been shown in studies to have a positive impact on IVF outcomes (1). According to a 2014 study, vitamin D3 modulates reproductive processes in both men and women. The study concluded that `in women undergoing in-vitro fertilization, a sufficient vitamin D level (≥30 ng/ml) should be obtained as this is associated with higher pregnancy rates. Vitamin D supplementation might improve metabolic parameters in women with PCOS. A high vitamin D intake might be protective against endometriosis’ (2)

Typical symptoms of vitamin D deficiency include Infertility, excess sweating, muscle weakness, chronic infections, weak bones, bone pain, chronic pain, tiredness, depression (it affects the level of serotonin in the brain), digestive issues, and asthma.

To allow your skin the opportunity to make vitamin D, it is recommended to spend 10 - 15 minutes every day out in the sunshine with no sunscreen throughout the year. In summer it is best to avoid the heat of the day so before 10 am and after 3.00 pm. Your skin will manufacture vitamin D when it is in contact with the sun.

If you are trying to conceive as a minimum it is recommended to take 1,000 – 2,000IU of vitamin D3 per day (preferably with K2 as they work as a team for bone health). Cod liver oil is a great source of vitamin D as well as vitamin A and important omega 3 essential fatty acids.


Selenium is an important antioxidant that helps to protect cells from free radical damage. It is a mineral that is low in New Zealand soils so many people are deficient.

Selenium is a powerful antioxidant that helps to support a strong immune system and regulates thyroid function by being involved in the conversion of T4 (thyroxine inactive thyroid hormone) to T3 (triiodothyronine the active thyroid hormone) in the liver. Selenium is also an important mineral for egg production.

Having adequate selenium in your diet is important if you have an autoimmune condition such as Hashimoto’s Thyroiditis, Celiac Disease, Crohn’s Disease, Lupus and Psoriasis) as it regulates excessive immune responses and chronic inflammation. If you are over 40 and trying to conceive, selenium may help to reduce the risk of having a child with congenital abnormalities.

One of the best ways to get selenium in your diet is to eat 3 Brazil nuts per day as Brazil nuts contain an average of 68 -91 mcg per nut. Other food sources are tuna, sardines, grass-fed beef, liver, chicken, egg, spinach.

Some of the common deficiency signs are hair loss, discolouration of nails and skin, tiredness, brain fog, hypothyroidism, infertility, poor immunity, and autoimmune diseases.

The Recommended Dietary Intake (RDA) for Selenium is 150mcg in total from all supplements (due to the risk of toxicity with very high amounts). In some instances, a higher dose may be recommended under the guidance of a qualified practitioner.

Uterine Natural Killer Cells

Natural killer cells (NK) are defined as `large granular lymphocytes (white blood cells) and are an important component of the innate immune system. Natural killer cells function as one of the first lines of defense, providing protection against viral and bacterial infections and helping detect and limit the development of cancerous growth’ (3)

As well as in the blood natural killer cells can also be found in the uterine lining, known as CD56 + Uterine NK Cells. ` CD56 uterine Natural Killer cells are present in human endometrium prior to the initiation of pregnancy and markedly expand to become progressively more granulated during the progesterone dominated secretory phase after ovulation and throughout the first trimester’ (4)

There have been suggestions in early studies that an elevated number of uterine natural killer cells are responsible for early pregnancy loss, as the natural killer cells essentially attack the uterine lining and developing embryo which causes implantation to fail. However, more recent studies have been inconclusive so it looks like there is still a lot to learn about this area. The theory of elevated natural killer cells did resonate with me when I was suffering from recurring pregnancy loss though and is something I investigated quite a bit although there didn’t seem to be anything conclusive in terms of what can be done to reduce these other than prescribed immunosuppressant medications which was not an option for me.

I discovered from my research that some of the biggest factors that lead to an increase in natural killer cells are autoimmune conditions, inflammation, stress, and thyroid imbalances. I always felt that I had all of these going on under the surface, but not always evident with testing. Testing thyroid antibodies to check for autoimmune thyroid issues such as Hashimoto’s is crucial if you are suffering from recurring pregnancy loss as this could be what is elevating those natural killer cells. I tried really hard at the time to get my thyroid antibodies tested but kept hitting a brick wall as my TSH and Free T4 were in the normal range. Luckily nowadays you can order your own Comprehensive Thyroid Check through a company called i screen nz (see the references at the end for the link to their website). I so wish this was available when I was trying to conceive, it may well have saved me a lot of time and heartache. I spent about 10 years working on my thyroid on and off with different supplements and dietary approaches.

Modulating the immune system

I wondered what I could do naturally to try and modulate my immune system between conception and implantation to potentially reduce an excess of natural killer cells in my uterine lining if that was what was happening with me. I tried many things over the years, different supplements, strains of probiotics, and dietary approaches but nothing really changed until 2018 when I conceived naturally at age 43.

Here is a summary of what I tried in the 6 months leading up to conceiving my daughter which could have helped to calm down my immune system allowing the pregnancy to progress:

  • Spore forming probiotics to regulate the immune system

  • Vitamin D as an immune modulator - I needed a therapeutic dose of this daily and I never took any less than 2,000iu per day. I knew when I was low in vitamin D as my feet would get restless and tingle.

  • A blend of Shitake and Reishi mushrooms - this was to help regulate potentially elevated natural killer cells.

I took these up until I discovered I was pregnant at around 5 weeks then stopped the mushrooms but continued with a therapeutic dose of vitamin D and probiotics throughout the rest of my pregnancy.

The role of the gut microbiome

The gut microbiome plays a key role in modulating your immune system, particularly in terms of keeping the two main arms of the immune system (T Helper 1 and T Helper 2) in a healthy balance. If the TH1 arm of the immune system becomes more dominant a person is more prone to autoimmune conditions. If TH2 is more dominant a person is more prone to allergies such as hay fever and eczema.

Probiotics can help to modulate the two arms of the immune system, especially during the early stages of pregnancy when the immune system is under a lot of stress. Although I don’t know exactly why I got pregnant naturally after 10 years of having recurring chemical pregnancies, one thing I did note is that I did start taking spore-forming probiotics about 3 months before I conceived and I did notice almost immediately a positive change in my skin health. I have had issues with eczema and skin rashes on and off since my mid 20’s after I caught a skin infection from a jacuzzi and ended up on antibiotics for 2 months. The spore-based probiotic I took was Megasporebiotic from Microbiome Labs. I wonder if the spore-based probiotics had a positive effect on balancing my immune system where other probiotics were unable to do.

Shitake and Reishi Mushroom for immune modulation

I took a mushroom powder with Shitake and Reishi to see if this would help modulate my immune system. Reishi mushroom dampens down an excessive immune response, which is common in autoimmunity, by restoring Th1/Th2 balance. It is also anti-inflammatory and supports the adrenal glands by having an adaptogenic effect. Shitake increases secretory IGA levels and reduces inflammation so is beneficial for inflammatory conditions such as endometriosis and uterine fibroids. It down-regulates inflammatory responses and has a beneficial effect on the gut microbiome. I stopped taking it as soon as I found out I was pregnant but I do wonder whether it was enough to keep my immune system from attacking the uterine lining so that implantation could naturally occur.

Food intolerances

What we eat plays an important role in the process of implantation as what we eat can have a direct effect on our immune system, especially if we are eating inflammatory foods or foods that we are intolerant to. Eating foods that cause a reaction can put extra stress on the immune system which can lead to immune dysregulation over time. Investigating and eliminating food allergies and intolerances are important if you are suffering from recurring chemical pregnancies and early pregnancy loss as you want to ideally remove anything that is triggering the immune system. I used to test myself for food sensitivities every few years to see if there was anything putting extra pressure on my immune system.

Inflammation is often to blame

When something goes wrong with the body, inflammation is often to blame. So, it is essential to protect yourself against inflammation by eating plenty of nature’s greatest anti-inflammatory, which is Omega 3 Essential Fatty Acids.

As well as reducing inflammation, omega-3 essential fatty acids have been shown to help fertility by helping to regulate hormones in the body, increase cervical mucous, promote ovulation and improve the quality of the uterus by increasing the blood flow to the reproductive organs. It is an important structural element of cell membranes in the ovaries. Good food sources of Omega 3 are Cod Liver Oil, fish, and flaxseed oil.

Summary checklist - eight areas to investigate

So in summary, recurring chemical pregnancies can be a very frustrating and lonely journey with very little support from medical specialists as it is all over so early. If you are suffering from recurring chemical pregnancies as I did, I would recommend considering the following options:

  1. Investigate autoimmune diseases that could be triggering your immune system. Push for the antinuclear antibodies (ANA) test if you haven’t had one yet to see if you have elevated autoantibodies attacking your body tissues. It is especially important to also get screened for Antiphospholipid Antibodies (APA, to see if blood clotting is an issue), Coeliac Disease, and autoimmune thyroid disease (Hashimoto’s or Graves). If necessary consider paying privately for a Comprehensive Thyroid Check including TP0 antibodies using the i screen nz service (see link in references)

  2. Investigate food intolerances that also could be triggering your immune system.

  3. Support your gut health with a spore-based probiotic

  4. Look at taking Vitamin D and selenium to modulate the immune system

  5. Support healthy methylation with methylfolate and look at getting your B12 checked to see if you need this as well. See previous blog posts on Folate and B12.

  6. Consider medical mushrooms like reishi and shitake for immune modulation if needed

  7. Reduce inflammation with Omega 3 Essential Fatty Acids

  8. Support stress levels with deep breathing, meditation, and fertility yoga. See my previous blog post for more on stress and adrenal support here.

Reach out if you have any further questions. I am happy to help.


  1. Grzechocinska B et al, The role of Vitamin D in Impaired Fertility Treatment, Neuro Endocrinol Lett, 2013, 34 (8) 756 – 62

  2. Lerchbaum E, et al. Vitamin D and Female Fertility Curr Opin Obstet Gynecol, 2014 Jun, 26/3) 145 -.

  3. Leischner C, Burkard M, Pfeiffer M, et all. Nutritional Immunology: Function of Natural Killer Cells and their modulation by Resveratrol for Cancer Prevention and Treatment. Nutrition Journal 4/5 2016

  4. Gaynor LM, Colucci F, Uterine Natural Killer Cells: Functional Distinctions and Influences in Pregnancy in Humans and Mice. Immunol 24/4/2017

  5. Comprehensive thyroid test via i-screen NZ which includes: SH, T4, T3, Reverse T3, thyroid antibodies -


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