The Top 5 Birth Control Pill Side Effects – Functional medicine options


Birth Control PillsBy Dr. Justin Marchegiani

Birth control pills can have many side effects. Many times birth control pills are prescribed for reasons outside of just avoiding pregnancy. Many times birth control pills are prescribed for acne, migraines, excessive menstruation and PMS symptoms.

The problem with this type of approach is it doesn’t fix the root cause of why those symptoms are there in the first place. At some point, these old symptoms will reveal themselves again and maybe worse than they were originally.

Today’s video is going to be on birth control pills and their side effects. We’re going to break down their mechanism, how they work and the potential side effects and just things that you can do naturally to get to the root cause.

Birth Control Pills

Birth Control Pills

The conventional alternative if you’re trying to prevent pregnancy is typically the chemical modality or the chemical pharmaceutical option, which is a birth control pill.

There are couple of different kinds that are out there.You have the shots, you have the ones where they insert little things under your skin, little pellets under your skin. And then you also have the typical birth control pill that you swallow. You also have IUDs, too, that are more physical deflectants of birth control pill but you have the Marina, which is a synthetic progesterone IUD that goes through and prevents pregnancy.

Outside of that, you have your birth control pill, you typically have your synthetic estrogen, like your Ethinylestradiol, like the Yaz for instance, and then you have your combinations like Yaz, which is an Ethinylestradiol and the Drospirenone. And then you have your regular estrogen-based birth control pills which are the Ethinylestradiol like the NuvaRing, etc.

The most prescribed medications out there are going to be your birth control pills, typically the combo, or the estrogen only. And sometimes you’ll even see synthetic progesterone ones that are done if you kept side effects with the combo progesterone and estrogen versions.

If you have those issues, if you’re trying to prevent pregnancy, that’s the typical avenue.

Are you on a birth control pill but would like more natural options? Click here to consult a functional medicine expert!

Other Uses of Birth Control Pills

Uses Of Birth Control Pills

Birth control pills are also prescribed for other side effects like acne or mood issues like in your period, migraine headaches, excessive menstruation, and a lot of those issues are driven by other physiological imbalances. So if you have breast tenderness or PMS symptoms (moodiness, back pain, breast tenderness, headaches), typically that’s going to be caused by fluctuations in estrogen and progesterone especially in the last half of your cycle. That will be about one to two weeks before you menstruate when you start seeing imbalances.

How Do Birth Control Pills Work?

Effects of Birth Control Pills

Lets talk about the organs involved when taking birth control pill. We have your cervix, vagina and uterus. So this is your vaginal area. Obviously what’s going to happen? You take a birth control pill, a few things are going to happen.

Decrease in FSH and LH

These are your pituitary hormones that talk to the ovaries to make progesterone and estrogen. When you’re taking a birth control pill, essentially you’re telling your brain that you’re pregnant. That’s why these hormones start to drop. When these hormones drop, they stopped talking to the ovaries to make estrogen and progesterone. So typically, FSH is going to then talk to the egg here and stop that egg from growing if it’s low. It’s going to stimulate the egg grow if it’s high. So the FSH is low, that egg is not going to grow. So the egg here won’t grow and then with the FSH being low and the LH being low, what tends to happen is you get a thickening of the cervical cap so it’s harder for sperm to make their way in to the uterine lining, and typically with a birth control pill, with natural cycle, estrogen start to come up in the first half of the cycle and that starts to thicken the uterine lining.

But when you’re taking like a Yaz pill for instance that has the synthetic progesterone, the Drospirenone, that actually thins out the uterine lining. It thins it out and makes it thinner, so it makes it harder for an egg if it is released to actually stick into the uterine lining. It makes it harder to stick.

Mechanisms Involved

Number one, it’s inhibiting ovulation by decreasing FSH and LH. That’s the first linchpin. If mechanism two and three doesn’t work and that works, we’re fine. But let’s say an egg, for some reason, does slip out. Let’s say the FSH and LH wasn’t quite low enough. Well, then maybe the egg pops out but maybe it’s still harder for the sperm to get in. So maybe number two prevents pregnancy from happening, and maybe number three, let’s say the sperm does make its way in past number two, and that’s when number two fails, maybe the egg can actually still bind into the uterine lining. But if it’s thinner, it’s going to be much harder for it to bind in.

So kind of recapping here, birth control pill works a couple different ways:

  1. Inhibiting ovulation.
  2. Preventing sperm from getting into the uterus area to begin with.
  3. Preventing the sperm and the egg from sticking into the uterine lining and fertilizing.

Women’s Menstrual Cycles

We typically have the first half of the cycle predominated by estrogen. So estrogen is up like this in the first half of the cycle; then we have progesterone that predominates the second half of the cycle. And you can see what happens is progesterone rises and falls and estrogen rises and falls right at the end of the cycle which triggers menses.  And then we have the part here in the middle of the cycle where ovulation happens and that’s where pregnancy can occur.

Effect of Pill on the Cycle

So basically what’s happening with the birth control pill is these hormones aren’t going to fluctuate because the LH and the FSH is dropped. Because the LH and the FSH is dropped, we’re not going to have that nice, natural rhythm of hormone because essentially our brains think we’re pregnant. That’s the general gist there.

What the birth control pill is doing is, instead of there being drops in progesterone level, we are now getting a high amount of progesterone and estrogen above where we’re supposed to be at. And so, we now have a flat line. Instead of having those perturbations, now it’s flat and smooth. And then typically around Day 21 and 22, we take those five to seven days of reminder pills which then allows the hormones to drop like so and that allows menstruation to happen. With progesterone only pill, that may not happen; but on an estrogen or estrogen-progesterone combo, that’s what’s going to happen. So that gives you the general physiological mechanism of how all this stuff is working.

Side Effects of Birth Control Pills
Birth Control Pills Side Effects


With the birth control pill, we may have more depression. It may affect your mood and it’s one of the most common side effects of the birth control pill because you’re affecting hormones. Hormones are intimately connected to our moods. So if you’re taking hormones and bringing them above a physiological or bringing them to a super physiological level, it may affect our moods.


Again, candida and fungal overgrowth. Because the birth control pills affect the pH in the vaginal tract, it makes it a little bit alkaline so it actually raises that pH a little bit.  When the pH is more alkaline above 7, that makes it more inhabitable for yeast and bacteria to grow. So when you’re stressed and when you’re on birth control pills, increased chance of a UTI or a fungal infection and then guess what happens? You’re given antibiotics and then what happens again? You’re at an increased chance for a rebound overgrowth. So you can see how one thing kind of increases your chance of intervention that drives other symptoms down the road.

Nutritional deficiencies

Birth control pills are notorious for creating B vitamin deficiencies, folate, B9, B12, B1, thiamine, riboflavin, niacin. All these are important. B vitamins, vitamin C vitamin E, zinc, magnesium, selenium are really important for your thyroid as well. So you can see these nutrients are going to be depleted with the birth control pill. You have to be mindful that if you’re going to use the pill, you have to make sure you’re taking high-quality multivitamin. That will replete some of these missing nutrients as well as a healthy diet on top of that.

Decreased libido

Because your birth control pill is increasing sex hormone-binding globulin, that’s going to bind up testosterone. So if here’s your testosterone compound like this, what it’s going to do is it’s going to bind the protein to it. So here’s the protein and it’s called sex hormone-binding globulin and that makes it harder for that testosterone to bind into the receptor site. Here’s the receptor site over here and because the purple guy is attached to it, it won’t quite fit. So that protein there renders your testosterone or your sex hormones to be a little bit lower functionally. So guess what happens? Libido goes downhill and also because the testosterone drops a little bit, guess what happens to women’s skin on the birth control pill? It tends to get a little better.

That’s why the birth control pill is prescribed off-label for mood. It can be prescribed for mood in the cycle because it at least levels out the hormones, so it may make it more level. A lot of women report more mood issues.

Weight Gain

This is kind of a controversial one. A lot of places say birth control does not affect weight gain at all but if you look at the side effects on the bottle or on the drug, it’s going to say weight gain. Now some of the mechanisms of that are estrogen, synthetic estrogen increases insulin resistance. So it causes the insulin in your body to make to have to make more of it because the cells are getting numb to the insulin. You go ding dong, ditch your neighbor, after a couple times they stop opening the door. Maybe after one time if they’re smart.

So that’s kind of what happens with insulin. Your body starts to make some of it, and then it’s saying false alarm, and then stops bringing the blood sugar in. So then you need more insulin which causes the fat cells to grow. Insulin is a storage hormone and causes fat cells to grow.

Thryoid Issues

Also sex hormone-binding globulin and thyroglobulin are increased. So thyroglobulin is another hormone where in my analogy over here with testosterone. This is going to be the thyroid hormone. So the T for testosterone, we have TH for thyroid, and then we have the P over here, this is the protein. This is thyrobinding globulin which is a protein compound and that’s going to make it hard for that thyroid hormone to bind into the receptor site over here, so it makes the free fraction, the bioavailable thyroid hormone to actually decrease. So we actually have less the thyroid from a functional standpoint.

Increased risk of Cancer

Birth control pills may increase cervical cancer 300%, 3 times, and increase breast cancer 2 times. This is a new study that came out in August of this year. Previous studies have said it decreases cervical cancer and ovarian cancer, but increases breast cancer. Now some other studies are showing the opposite. We’re saying breast cancer is 2 times higher; but now we’re saying cervical cancer may even be 3 times higher. And that’s from an Iranian study.


Fix the root cause. If you’re taking a birth control pill because you’re trying to prevent pregnancy. Fine, I get that. It totally makes sense. Take a look at the natural birth control pill video if you want to avoid the synthetic hormones and some of the potential side effects, I recommend using that.

We don’t want any unwanted pregnancy, so that’s your only option that you’re willing to do, or that you can be compliant with. Fine, I get it. It’s there for you. Make your choice. I just want you to be informed so you know the potential side effects. Also, you know the other natural options by watching my other natural birth control pill video options. We’ll put on screen so you can access.

And if you’re having these other symptoms like depression, or mood issues, or excessive bleeding, or you’re having weight gain, or skin issues, let’s say as an off-label prescription for the birth control pill, well, you really want to get to the root cause with functional medicine. This invovles getting the adrenals, getting your hormones, and getting your cycle looked at and balanced out.

To find out more about more natural ways to prevent pregnancy, ask a functional medicine expert HERE!

If you’re trying to get your hormones balanced, or trying to get yourself back on track hormonally from some of the side effects of being on birth control pill, or trying to avoid it, click on screen, subscribe. You can always schedule a consult with myself.

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The entire contents of this website are based upon the opinions of Dr. Justin Marchegiani unless otherwise noted. Individual articles are based upon the opinions of the respective author, who retains copyright as marked. The information on this website is not intended to replace a one-on-one relationship with a qualified health care professional and is not intended as medical advice. It is intended as a sharing of knowledge and information from the research and experience of Dr. Justin and his community. Dr. Justin encourages you to make your own health care decisions based upon your research and in partnership with a qualified healthcare professional. These statements have not been evaluated by the Food and Drug Administration. Dr. Marchegiani’s products are not intended to diagnose, treat, cure or prevent any disease. If you are pregnant, nursing, taking medication, or have a medical condition, consult your physician before using any products.