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The Undiscussed Side Effects of Birth Control

Hormonal contraceptives are used by over 100 million women worldwide. They are, however, most often used by women in the western world.

Of the available hormonal options, the combined oral contraceptive pill (OCP), also known as “the pill” or birth control pill, is the most common choice, with 4 out of 5 sexually active women reporting either current or previous pill use.

Although OCPs are a highly effective form of birth control and have been revolutionary for women, like all medications, they come with side effects, many of which are rarely discussed between women and their healthcare providers.

It is important for women to have a clear understanding of both the pros and cons of using birth control, relative to their individual existing health factors.

Within my integrative health coaching practice I see far too many women coming to me with a myriad of negative health issues stemming from long term use of birth control.

What’s more- most of the women who reach out to me were honestly unaware that their hormonal imbalance, gut dysfunction, GI struggles, weight loss troubles, nutrient deficiencies, hypothyroidism, anxiety or depression was even related to- or could be related to- their birth control.

The truth is that there are consequences from daily doses of synthetic, chemically-altered hormones, and I’d like to explore those consequenes in this blog.

First, I’d like to mention that in no way do I want this blog to infer that I am opposed to the use of birth control. I am not. By sharing this information I am in no way trying to make any woman feel shameful about a decision she might have made for herself to use birth control. I simply want to bring to light what science has to say about how birth control impacts the female body, so that women considering birth control, using birth control, or who are contemplating stopping birth control, have the information they need to make the best choice for themselves.

Birth Control Options There are many options for preventing pregnancy, but for the purposes of this blog I’m only going to discuss hormonal short term (pill, patch, etc) and long term (IUDS, etc) birth control.

Both short and long term forms of hormonal birth control involves adjusting your body’s natural estrogen and/or progestin levels to make pregnancy much less likely.

Common short term methods include birth control pills you take every day, a patch you replace every week, a vaginal ring you change every month or a shot your doctor gives you every three months. All of these methods require a prescription. For most women, they’re about 91% to 95% effective at preventing pregnancy.

Interestingly enough many women who use birth control reported having either requested it or been prescribed it not as means of pregnancy prevention but in attempts to “regulate” their cycle, decrease the intensity of their cycle or worse- even suppress their cycle(!!???).

Dr Lara Briden, who has written extensively on womens hormonal health says that “To say that women don’t need ovulation except to make a baby would be like saying that men don’t need testosterone except to make a baby!Women need natural periods because regular ovulatory menstrual cycles are how women make hormones.

Long-term contraception can be a good choice if you want effective, lasting birth control without much maintenance. Choices include an implant inserted into your arm or an intrauterine device (IUD) inserted into your uterus. These methods are 99% effective at preventing pregnancy. They’ll work for 3–10 years, depending on the particular method you choose. The implant (Nexplanon) and hormonal IUDs (such as Skyla, Mirena, Kyleena) work by adjusting your body’s progestin levels over time. Copper IUDs (ParaGard) do not use hormones. Instead, the copper stops sperm from fertilizing your eggs.

How Birth Control Works

Combined OCPs have both an estrogen analogue, ethinyl estradiol, and one type of progestin.

There are many different forms of progestins which all have slightly different properties, but the ethinyl estrogen is fairly standard.

By adding the ethinyl group to the estrogen it alters the compound, allowing it to be absorbed better orally, but also makes it significantly more potent in the blood, with a stronger affinity to bind estrogen receptors.

This means it acts differently from our naturally occurring estrogen. However, it is actually the progestin component that is responsible for contraception.

The progestin works by inhibiting ovulation, thickening the cervical mucus to inhibit sperm penetration and altering the uterine lining to be unable to support implantation.

Any doctor who tells you otherwise is lying. If progesterone and progestins were the same why do fertility doctors always use progesterone and not progestin? If the two were the same why don’t synthetic progestins show up in blood and saliva tests of progesterone levels? In other words if the two were one in the same then why wouldn’t taking progestins raise progesterone in the body?

Suggesting that synthetic, not-found-in-nature hormones will work as well as, or better then your own hormones is saying like breaking down the front door to get inside your home is identical to putting the key into the lock and turning the knob. You get the same end result- being able to get inside- yet you pay a heavy price if you choose the option of breaking down the door. The same applies to using synthetic hormones. They have “some” of the same effects as your natural hormones but not without a heavy dose of unwanted short and long term side effects.

In fact the main reason women choose to discontinue hormonal contraceptives are because of side effects, like mood disturbances, decreased libido, weight gain, gut problems, hormonal or endocrine issues, poor bleeding control, and the fear of side effects.

These are the very side effects I want to discuss here. They get little attention and can often be ignored by medical professionals.

I want women to be well informed of the potential problems hormonal birth control can cause so they can choose their course of action appropriately.

1. Nutrient depletions

Nutrient depletions caused by the pill are an important topic to discuss, as they may contribute to many of the other side effects of the pill and may explain the lasting impact of those side effects as well.

It is difficult to diagnose nutrient depletions caused by the pill, as depletions don’t occur instantaneously. Rather nutrient depletion happens slowly over time and the consequences, like fatigue or low energy (common female complaints), can take a while

to surface.

There is, of course, downstream consequences of being depleted in key micronutrients as well. These consequences can manifest in a variety of ways such as increased inflammation, decreased immunity, hormone and thyroid dysfunction, etc.

When nutrient levels are measured in the blood of pill-users and compared to non-users, it has been shown that there are significant depletions in vitamins B1, B2, B3, B6, B12, folic acid, C, and E; minerals magnesium, selenium, and zinc; the amino acid tyrosine and the powerful antioxidant coenzyme Q10 (CoQ10).

Even the World Health Organization states that clinicians should be carefully monitoring and supplementing vitamins and minerals in women on hormonal contraception as a first-line approach.

Yet how many womens doctors are honestly doing so? Running nutrient panels to check for key nutrient depletions and then addressing via either strategic dietary measures or supplementing accordingly?

It is currently unclear as to why the pill causes depletions. It has been hypothesized that the delicate cells in our digestive systems were not meant to be exposed to orally ingested, synthetic hormones, and that this impairs adequate nutrient absorption.

Evidence also suggests that the estrogen and progestins increase the activity of liver enzymes, which require many nutrient co-factors.

Nevertheless, nutrient depletions are common in pill-users and can be easily addressed via a nutrient-dense dietary pattern and targeted supplementation.

2. Depression

The use of hormonal contraceptives, especially among adolescents, has been positively associated with a diagnosis of depression and the subsequent use of another (and often unnecessary) medication- antidepressants.

I know it’s old, but a solid 2005 study found that women on the pill had depression rates that were TWO TIMES as high as non-users.

This is interesting because research shows that mood symptoms are a recognized reason for discontinuing birth control pills, meaning this data - while significant- may actually even be underestimating the possible influence that birth control pills have on depression.

There are a few ideas that have been proposed to understand this birth control pill-mood connection.

First, about 80% of all women using birth control pills for 6 months or more have been shown to experience abnormal tryptophan metabolism, reducing their ability to make serotonin, our “happy hormone.”6 This is likely due to the depletion of vitamin B6, which is required for the production of serotonin from tryptophan.

Further, most of the body’s serotonin is produced in the gut. Yet the use of hormonal birth control actually changes the pH of the gut, creating an environment vulnerable to pathogens and infections. There is also a strong connection between birth control and increased intestinal permeability (leaky gut). With impaired gut health, serotonin production is therefore impaired as well.

Further, progestins have been found to increase levels of monoamine oxidase, which breaks down serotonin, which compounds this effect.

Other nutrients that may be involved in the depressive effect of the pill include vitamin B12, folic acid, and tyrosine, which are responsible for creating neurotransmitters that regulate mood and emotions.

3. Lowered libido

These sexual side effects are one of the most common reasons that women stop taking the pill.

While all progestins inhibit ovulation by interacting with the progesterone receptor, progestins can also bind to receptors for other steroid hormones, such as the androgen and glucocorticoid receptors.

By binding the androgen receptor, the pill decreases the production of testosterone from the ovary, reducing the amount of free testosterone available.

Testosterone is as vital in women as it is in men, especially with regards to libido. Testosterone is the hormone that controls sex drive in both men and women and so, a decrease will lower libido.

Additionally, the pill acts on the liver at a genetic level, causing an upregulation of sex hormone-binding globulin (SHBG).

An increase in SHBG means more testosterone will be bound, resulting in even less free, active testosterone available.This explains why the pill is very effective at reducing acne, a common reason women choose to start the pill.

A study from the Journal of Sexual Medicine found that women on the pill have SHBG levels FOUR TIMES higher than never-users; moreover, even after 6 months of being off the pill, SHBG remained TWO TIMES higher, which helps to explain the long-term sexual dysfunction than some women experience even after discontinuing birth control pill use.

4. Gut microbiome disruption, leaky gut, and inflammation

It has been established that birth control pills have an impact on the vaginal microbiome, as it is well documented that the pill increases the incidence of vaginal yeast infections.

But the association between oral contraceptives and intestinal inflammation has been around for decades. It first reported in the late 1960s.

It was found that birth control pill use was associated with Crohn’s disease, and discontinuation of the pill demonstrated resolution of the disease. More recent research found that the use of birth control pills is associated with an almost 50% increase in the risk of developing Crohn’s disease.

Again, the exact mechanism remains unknown, but multiple hypotheses have been suggested First, oral estrogen has been shown to modulate intestinal permeability, altering the barrier function of the gut. Secondly, exposing the digestive tract to exogenous hormones may disrupt the normal gut flora, creating dysbiosis.

Dysbiosis simply means an altered state of gut flora, or an unfavorable microbiome balance. Some of the main symptoms associated with it are:

  • Bloating

  • Diarrhea

  • Headaches

  • Abdominal pain

  • Mental fog

  • Constipation

  • Acne

  • Indigestion

  • Acid reflux

However, the impact of gut microbiome perturbations go well beyond merely affecting gastrointestinal health, as we now know that these microbes affect most of our physiologic functions from metabolic functions, protecting against pathogens, to educating our immune system.

Lastly, exogenous hormone use has shown to alter the immune system responses, leading to inflammation.16 When markers of inflammation are measured in the blood, like C-reactive protein (CRP), women who use birth control pills have levels TWO TIMES higher than non-users.

All of these effects together may lead to multifocal gastrointestinal dysfunction, but, it is not only the digestive system that will be affected by the inflammatory actions of the pill. It is now generally accepted that chronic low levels of inflammation may cause or advance many common diseases, so this effect is critical and likely wide-reaching.

5. Endocrine effects

Thyroid hormones Thyroid function also seems to be disrupted by the use of birth control pills and is likely why some women on the pill exhibit hypothyroid-like symptoms.

Studies show that women on the pill have an augmented response to thyroid hormones.

In women using birth control pills, thyroxine-binding globulin is significantly increased. This is the protein responsible for binding free thyroid hormones in the blood, and when elevated it can reduce the availability of active thyroid hormones.

Lower active thyroid hormone levels are associated with a decrease in metabolism, weight gain, difficulty losing weight, sluggishness and fatigue, increased cholesterol, and other physiological symptoms.

The thyroid may be further affected by birth control pills due to elevated estrogen which inhibits the conversion of thyroid hormones into their active form (converting T4 into T3).

Additionally, the thyroid requires both zinc and selenium to produce and convert thyroid hormones, and as I mentioned earlier in this post, these essential micronutrients are both commonly depleted by the pill.


Another interesting finding in women on birth control pills is the altered cortisol levels. When blood levels of cortisol were measured in women on the pill, there was significantly higher cortisol compared to non-users.

Chronically elevated cortisol levels are markers of permanent stress, which means the adrenal glands are constantly being overworked.

Moreover, the adrenal glands need B vitamins, vitamin C, and magnesium to optimally function, and because these micronutrients are depleted by the pill, the adrenals may suffer.

Insulin resistance

Birth control pills may also aggravate insulin resistance, which is important to note, as the pill is a common treatment option for women with polycystic ovary syndrome (PCOS).

It is suggested that long-term pill use may increase a woman’s risk of developing diabetes and heart disease.

Although this is of greater concern in women with PCOS, who are already predisposed to diabetes and heart disease, the effect is also seen in normal women using birth control pills.

The Bottom Line
  • Oral hormonal contraceptives are one of the most commonly used prescription drugs in the world, making a discussion of the potential, wide-reaching side effects (the well-known and lesser-known ones) and diverse physiologic consequences extremely important.

  • I personally feel healthcare providers and womens doctors need to be more thoroughly explaining to women the risks and side effects associated with both short and long term birth control use.Not to deter them necessarily, but to appropriately equip them to make well educated choices.

  • Hormones are powerful chemicals that have the ability to act on virtually every cell in the body, so using them shouldn’t be taken lightly.

  • If you're dealing with some of the hormone, immune, and gut symptoms I've mentioned, and you are using birth control, it's worth considering whether or not the cause of those issues, is in fact, the use of hormonal birth control.

  • Not only do we need to be aware of the effects of exogenous hormones once they enter the bloodstream, but also when they enter the digestive system, as for almost all of evolution, women did not swallow hormones orally. The gut is truly the gateway to health, and when it’s compromised it has a body wide impact.

If you’re considering birth control, using birth control, or even contemplating stopping birth control, it’s important to discuss potential side effects with your healthcare provider. Don’t be afraid to ask questions and request more information before making the best decision for you and your body.

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