A Doctor’s Guide to Birth Control Side Effects

Lilli Link, MD
July 24, 2019

Whether you’re currently on birth control, considering going on birth control, or trying to get off of it, here are the facts to be aware of —and the side effects of birth control you’ll find in the fine print of those pamphlets you always toss.

When birth control pills first came out in the 1960s, it was a game-changer for women as it gave them a simple way to put them in the driver’s seat for birth control. By enabling women to better determine when or if they have children, oral contraceptives and other methods of reliable birth control have helped make it possible for more women to pursue higher education, enter advanced professional fields, and earn higher wages.

But over the years we’ve learned that there is no such thing as a free ride. Just like with every other medication, there are side effects, both major and minor associated with birth control. With roughly 10 million women in the US taking birth control pills at any given time, and 1 in 4 girls 15-24 years old using it, even uncommon adverse events aren’t all that rare.

To decide what’s best for you, it’s important to know what some of the potential side effects of birth control are and what non hormonal birth control options are available.

What are birth control pills?

A birth control pill most commonly consists of a combination of synthetic estrogen and progesterone. There is also a progesterone-only version used in certain cases. The FDA first approved it as a form of birth control in 1960, and since then formulations have evolved to include much lower doses of hormones than they used to, making them equally effective with fewer serious side effects. The main way it works is by inhibiting ovulation (i.e. stopping the ovary from releasing an egg into the fallopian tube each month).

The good news is that when taken correctly, meaning no missed doses, it is extremely effective at preventing pregnancy, with fewer than 1 pregnancy for every 100 users each year . In reality, women do forget doses, and there are about 9 pregnancies per 100 users per year.

Hormonal birth control side effects

While birth control side effects are fewer than in the 60s, if you look at the package insert of a birth control pill , there are a number of less serious ‘adverse reactions’ listed, none of which are a sign of a serious illness.

Side effects of birth control:

  • Nausea
  • Spotting
  • Bleeding between periods
  • Breast tenderness
  • Abdominal cramps and bloating
  • Edema (water retention)
  • Heavy bleeding or missed period
  • Melasma (dark pigmentation on the face) which may persist
  • Headaches
  • Migraines
  • Weight gain
  • Insulin resistance
  • Blurred vision or nearsightedness

Some of these side effects are temporary, lasting just a few months, and others are minor enough, such as mild insulin resistance. However, there are several more serious and potential side effects of birth control that deserve more attention.

Yeast infections

Research has shown that yeast infections are more common amongst women on birth control . While birth control pills don’t directly cause yeast infections, they can disrupt your body’s natural hormonal balance —specifically the balance between estrogen and progesterone—which can sometimes lead to yeast overgrowth and subsequent vaginal infection.

Gum disease and Crohn’s disease

Gum disease is a more common side effect of birth control pills and this may be because the Candida and Prevotella bacterial species that contribute to it are more abundant in the mouth when taking birth control.

Crohn’s disease, a form of inflammatory bowel disease, also occurs more often in women on birth control , perhaps almost three times as often. This may be a result of the change in gut microbes and estrogen’s negative impact on gut permeability.

Mental health and depression

In one randomized controlled study of 178 women, those on birth control experienced less premenstrual depression, but during other parts of their cycle were more likely to be anxious and moody. An observational study of over 1 million women in Denmark, found that women who took the pill with both estrogen and progesterone were about 20% more likely to end up on an antidepressant . There may even be an impact on cognitive function. According to one small study of 43 women, those on birth control pills had worse verbal fluency than those not taking a hormonal form of birth control.

Nutritional deficiencies

Additionally, though not listed on the package insert, there is some concern that various vitamins and minerals are depleted in birth control pill users . Studies have found lower levels of numerous vitamins (folate, B2, B6, B12, vitamins C and E) and minerals (selenium, zinc, and magnesium) in women taking birth control pills. One study focused solely on vitamin B12 and found birth control pill users had consistently lower vitamin B12 concentrations than non users, independent of their dietary intake.

Even if you are taking a multivitamin/multimineral while on birth control pills, there may still be concern that the deficiencies studied represent just the nutrients scientists have thought to test and that the pill could also be affecting other nutrient levels as well that you won’t find in a multivitamin/multimineral.


Inflammation , which is a common denominator in essentially all chronic disease , is also more likely with birth control pills. High sensitivity c-reactive protein , a measure of inflammation that we check routinely at Parsley Health, has been shown to be high more frequently among birth control pill users than non-users. That may help to explain the increased risk for cardiovascular events among birth control users.

Blood clots

Venous thrombosis (blood clots) is one of the more serious negative side effects of most birth control pills. Venous thrombosis occurs when a blood clot forms in the vein, creating the potential to travel to the lungs and become life-threatening. Only about 2-4 out of 10,000 women will develop this kind of blood clot. But for those taking birth control pills, the risk increases about 3.5 times. The risk of a heart attack or stroke in women under 45 years old is also very uncommon. Nevertheless, birth control pills increase that risk by 60% at the lowest estrogen dose, and more so as the estrogen dose increases.


Gallstones, though typically not life-threatening, are deposits of digestive juices within the gallbladder that can cause symptoms like pain, indigestion, nausea, and vomiting. About 5% of women under the age of 40 have gallstones , but since estrogen and progesterone increase gallstone formation , the likelihood of developing gallstones is 35-50% higher for women who take birth control pills compared to women who don’t. Having gallstones becomes a significant quality of life and health issue, as gallstones can be painful and lead to surgery to remove the gallbladder. Ultimately this has a negative and life-long impact on digestion and your microbiome.

Decreased sex drive

Another listed side effect of birth control pills is that for a small percentage of women, it can significantly diminish sex drive . A likely explanation is that birth control pills decrease the amount of testosterone circulating in your body. A study validated this when comparing the sex drive of participants using a contraceptive ring, implant, or birth control pill to those using a non hormonal birth control option, such as a copper IUD, finding that participants using a hormonal birth control option experienced a decreased sex drive .

Benefits of birth control pills

Besides being an effective means for birth control, studies show that birth control pill users have a decreased risk for ovarian, endometrial , and colorectal cancer when compared to non users. The pill has also been seen as a useful method for chemoprevention across women with varying levels of cancer risk. Other potential advantages of birth control pills include lighter, less painful periods, more regular periods, and less acne (with some forms of birth control pills).

Often doctors will prescribe the pill to address symptoms such as painful periods, acne, migraines, and excessive hair growth, but at Parsley Health we aim to address the underlying causes. Once we do that, it frees our patients up to pick the best birth control method for their needs.

Birth control alternatives

For those who decide they don’t want to deal with the potential side effects of birth control pills, there are other birth control options, including condoms, non-hormonal copper IUDs, diaphragms and various types of fertility trackers. Here’s our take on the options we often recommend to our members at Parsley Health who don’t wish to be on hormonal birth control.

Non hormonal IUDs

A non hormonal IUD is typically made of copper and works by altering the way the sperm swims, preventing it from meeting an egg and therefore preventing pregnancy. They can last up to 12 years or be removed at any time. We see that patients find non hormonal IUDs best for when they don’t foresee getting pregnant anytime soon or are done having children.

Digital fertility trackers

Apps like Natural Cycles and Clue Period Tracker can help you learn about your own cycle, predicting ovulation, your next period, and when you’re most fertile, sending you alerts accordingly. You can also track your basal body temperature (AKA your body temperature at rest) within the app. Slight increases in your basal body temperature often signal a period of ovulation. We find that patients who are transitioning off a birth control pill or trying to get pregnant find a fertility tracker app the most effective non hormonal birth control option.

Final thoughts on the birth control pill.

For some women, there are individual and personal reasons that make birth control pills the best choice of birth control for them. But the above information makes it clear that the decision to start or continue using birth control pills is a serious one with many potential short and long-term effects. It deserves thoughtful consideration by the patient and the doctor before choosing it. If you decide hormonal birth control is the best option for you, there are also options outside of the pill that you can speak to your doctor about, such as contraceptive patches, implants, and hormonal IUDs .

It is wonderful that women have these choices for birth control. I hope this information not only keeps you in the driver’s seat for contraception but also helps you know where you are going.

Lilli Link, MD

Dr. Lilli Link is a board-certified Internist and Functional Medicine Practitioner who graduated from medical school at the University of Chicago, and completed her residency at Columbia Presbyterian Medical Center in New York.

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