Hormonal birth control does more than prevent pregnancy. If you’re using combined oral contraceptives (COCs), it can also change what shows up in your blood tests—from your vitamin levels and cholesterol to inflammation and hormone markers.

These changes don’t always mean something is wrong. But birth control can shift your baseline, and that matters when you’re tracking your health through lab results. 

Here’s what you should know about the biomarkers affected by birth control and what they mean for your health.

Nutrients Drop While You're on the Pill

The birth control pill you’re taking can lower your body’s levels of several essential nutrients, even with a healthy diet. This is one of the most overlooked ways in which birth control affects nutrient levels:

• Vitamin B6, B12, and folate

These vitamins help with energy, mood, and red blood cell production. Vitamin B6, B12, and folate tend to drop in women using birth control pills, especially with long-term use, which may lead to symptoms like fatigue, brain fog, or numbness. Learn more about symptoms of low vitamin B12 here.

• Vitamins C and E

Both protect your cells from oxidative stress, which can damage DNA, proteins, and lipids over time. Lower levels of vitamin C and E may leave your body with less antioxidant defense.

• Magnesium, zinc, and selenium

These minerals support your immune system, stress response, and metabolism. They also help regulate inflammation, thyroid function, and antioxidant defense. Studies show that magnesium, zinc, and selenium are often lower in women using COCs, possibly due to changes in absorption, metabolism, or increased demand.

If you’re feeling tired, foggy, or run down while on birth control, nutrient testing is a good place to start.

Cholesterol, Blood Sugar, and Inflammation Can Shift

Hormonal contraceptives also affect your metabolic and inflammatory biomarkers.

• Cholesterol and triglycerides

Most pills raise LDL (bad cholesterol), triglycerides, and sometimes HDL (good cholesterol), depending on the type of progestin used. These shifts can make your cholesterol numbers look different on a blood test, even if your diet and lifestyle haven’t changed.

• Fasting glucose and insulin

Some women develop mild insulin resistance on the pill, especially if they already have metabolic risk factors.

• Inflammation markers like hs‑CRP

This is a key connection between hormonal birth control and inflammation. Many studies show higher hs‑CRP in contraceptive users, which signals low-grade systemic inflammation.

These changes are usually moderate, but they can still affect how your lab results are interpreted. If you're tracking your metabolic health, make sure your care team knows you’re on birth control.

Your Hormones Don’t Always Mean What They Seem

COCs change your hormone levels and how your body makes, uses, and transports them. That’s why checking hormone levels while on birth control often tells a different story than you might expect.

• SHBG (sex hormone-binding globulin)

That means less free testosterone and estrogen are available, even if total levels look normal. This impacts your mood, energy, and libido. This is one of the reasons many women feel tired or experience low libido while on COCs. The link between SHBG and birth control is strong, and it’s one of the most important markers to check.

• TBG (thyroid-binding globulin)

Birth control pills can affect thyroid test results. Contraceptives make your total thyroid hormones look high, even if your active (free) levels are low.

If you’re checking hormone levels while on COCs, focus on free hormone markers where possible.

The Pill Can Alter Your Stress and Cortisol Patterns

Birth control affects your stress response, too, especially when it comes to cortisol.

• Total cortisol levels

So, how much does birth control increase cortisol? It depends on the person, but studies show a 20 to 50% increase in total cortisol is common. This rise is due to increased cortisol-binding globulin.

• Free cortisol

Some women ask, does birth control increase cortisol or lower it? In truth, both can happen depending on which form you're measuring. In fact, some studies suggest that birth control use can lower the body’s stress reactivity, leading to a blunted cortisol spike. So, birth control lowers cortisol, too.

These changes are subtle, but they matter especially if you’re dealing with chronic stress, fatigue, or burnout.

Estrogen, Progesterone, and Thyroid Levels Are Suppressed

One of the most common lab findings in birth control users? Low hormone levels. The pill suppresses ovulation, which shuts down your natural production of several key hormones.

• Estradiol

This is your body’s natural estrogen. While the pill supplies synthetic estrogen, your own estradiol levels go much lower.

• Progesterone

The pill prevents ovulation, so you don’t make natural progesterone. Low progesterone levels affect mood, sleep, and cycle-related symptoms.

• Thyroid markers

Free T4 may go down while total T4 goes up. This doesn’t always mean there’s a thyroid issue, but it’s worth keeping an eye on.

If you're wondering whether birth control lowers estrogen levels or affects thyroid tests, the answer is yes, and both show in your labs.

What Else Can Change?

• Liver enzymes

Some birth control affects your liver enzyme levels, such as AST or ALT, especially over time. This is usually harmless but worth watching. It's one more example of how birth control and blood tests interact in ways you may not expect.

• Clotting factors

The pill can raise some clotting proteins, which may raise the risk of blood clots or stroke in certain individuals. These markers don’t always show up in basic panels, but they’re important in clinical decision-making.

What to Track While You’re on the Pill

If you're using COCs and want a clear view of your health, here are the biomarkers affected by birth control that are worth tracking:

• Vitamin B12, folate, magnesium, zinc

• Cholesterol and fasting glucose

• hs‑CRP

• Free T3, free T4, and TSH

• SHBG, estradiol, progesterone, testosterone, and cortisol
  
  
  

At Mito Health, we interpret your labs with context. If you're on birth control, we account for that in every panel and consultation, so you get insights that actually make sense for your body.

Interpreting Lab Results While on the Pill

Hormone levels on birth control change your internal landscape. It can shift nutrients, cholesterol, inflammation, hormone levels, and more. These changes aren’t necessarily dangerous, but they do matter, especially when you're using bloodwork to track your health.

Mito Health gives you access to comprehensive blood testing, personalized analysis, and guidance that accounts for your hormone use. Whether you're trying to optimize energy, improve your cycle, or simply understand what’s going on, we’ve got you covered.

Resources:

• https://pubmed.ncbi.nlm.nih.gov/1415443

• https://pubmed.ncbi.nlm.nih.gov/37419659

• https://www.ncbi.nlm.nih.gov/books/NBK588296

• https://pubmed.ncbi.nlm.nih.gov/24159692

• https://www.mdpi.com/1420-3049/26/4

• https://pmc.ncbi.nlm.nih.gov/articles