Women’s health: What are the “unknown” side effects of birth control pills?

Published Jun 4, 2021 • By Courtney Johnson

Since its authorization by the FDA in 1960, the oral birth control pill has been touted as one of the “best” solutions for women in taking control of their reproductive health. Beyond their ability to protect against pregnancy, oral contraceptives can help to control skin issues such as acne and regulate heavy periods and menstrual cramps, but there are also a number of significant side effects that are less discussed.

How do oral birth control methods work? What are the long term side effects of oral contraceptives? 

We explain it all in our article!

Women’s health: What are the “unknown” side effects of birth control pills?

How do oral contraceptives work?

Birth control pills are oral contraceptives that prevent sperm from coming into contact with, and therefore fertilizing, an egg. They contain hormones (progestin and estrogen for the combination pill, or just progestin for the “mini pill”) that prevent ovulation, so no egg is produced by the ovaries during the menstrual cycle. These hormones also thicken the mucus of the cervix, acting as an additional barrier to keep sperm from reaching an egg.

Typically a course of birth control pills contains 21 once-daily hormone pills, followed by 7 days of placebo (non-active) pills during which the woman will have her period. Over the years, different formulations have been developed, with some containing only 4 placebo pills for a shorter period or some containing none at all, allowing menstruation to be skipped entirely.

What are the benefits of birth control pills?

There are numerous benefits to oral contraceptives, the most evident of which is their effectiveness. If taken correctly, birth control pills are 99% effective at preventing pregnancy.

The pill also brings a number of beneficial side effects; both combination and progestin-only pills regulate a woman’s period, reduce the intensity of menstrual cramps and flow, and lower a woman’s risk for ectopic pregnancy (pregnancy in which the fertilized egg implants outside the uterus). It has also been found to prevent or diminish:

  • Acne
  • Premenstrual syndrome (PMS)
  • Cysts in the breasts or ovaries
  • Serious infections in the ovaries, ovarian tubes, or uterus
  • Endometrial and ovarian cancer
  • Bone thinning
  • Iron deficiency (anemia)

Oral contraceptives can also be a helpful tool in family planning, as a woman can get pregnant right away after stopping to take them.

Finally, one of the most cited benefits of birth control pills are their convenience - the pill is small and easily transportable and in one daily dose you are protected all day.

What are the short-term side effects of birth control pills?

During the first few months of taking birth control pills, the patient can experience a number of temporary symptoms as the body adjusts to the artificial progestin and/or estrogen. The most common symptom is minor bleeding in between periods, called breakthrough bleeding. This occurs most often in women taking the mini-pill, but can also happen if you miss a dose. Breakthrough bleeding tends to stop on its own, but if it continues or is accompanied by other side effects, make sure to report it to your doctor.

Birth control pills can also cause nausea and breast tenderness in some women, which may be reduced by taking the pill at bedtime.

Other short-term side effects can include:

  • Headache
  • Weight gain
  • Mood swings

What are some of the long-term side effects of birth control pills?

While the benefits of oral contraceptives are widely known, the potential long-term side effects are less talked about. For most women, taking birth control over a sustained period of time does not cause significant health issues, but there are a number of potential risks that may arise in the long term.


The natural female sex hormones (progesterone and estrogen) can affect the risk for certain types of cancer. In the same way, hormone-based contraceptives like the pill can increase or decrease a woman’s risk for certain cancers. 

According to the National Cancer Institute, hormonal birth control can increase one’s risk for the following cancers:

  • Breast cancer: Risk for breast cancer has been found to be slightly higher in people who use birth control pills than those who have never done so.
  • Cervical cancer: Being on the pill for more than 5 years has been linked with higher risk for cervical cancer, though most types of cervical cancer are caused by the human papillomavirus.

Cardiovascular issues

Birth control pills, especially combination pills, can increase one’s risk of serious cardiovascular issues, such as heart attack, stroke, and blood clots. In some women, birth control pills can also increase blood pressure. In women over 35, long-term use can increase the risk of thrombotic phenomena (blood clots), especially in those with pre-existing cardiac conditions or diabetes.

In case of uncontrolled high blood pressure or family health history of cardiovascular diseases, make sure to check with your doctor about other contraception options.

Gallbladder disease and gallstones

The gallbladder is a small, pouch-like organ positioned just under the liver. Its job is to store bile produced by the liver, which is then excreted from the gallbladder into the intestines to help with fat digestion and the absorption of vitamins

Birth control pills have long been recognized in research as contributing to the risk of gallbladder disease and cholelithiasis (gallstones). Gallstones occur when bile acids solidify into stone-like structures, leading to nausea, pain, and inflammation

Hormonal birth control pills can also impact thyroid function, which in turn plays a role in gallbladder health.

Low testosterone

We all have certain amounts of the male hormone testosterone in our bodies. Birth control pills, if taken over time, can lower this natural level of testosterone as they are metabolized through the liver. As the liver processes the oral contraceptives, it produces a protein called the sex hormone binding globulin (SHBG), which acts like a sponge, drawing testosterone out of the bloodstream and reducing “free testosterone”

While lower testosterone levels can have beneficial effects on the skin (reducing acne, etc.), it can also have an adverse effect on mental health, causing low mood and libido, among other symptoms.

This phenomenon can be avoided by using non-hormonal contraceptive options.

Nutritional deficiencies

Long-term use of birth control pills can lead to depletion of vitamin C, as well as other key vitamins like B12, B6 and folate, and minerals such as zinc, selenium, and magnesium. Low levels of these vitamins can significantly impact your mood, create fatigue, and lead to other symptoms, especially headache.

Crohn's disease

Oral contraceptives can also, surprisingly, increase one’s risk of developing irritable bowel disease (IBD), and Crohn’s disease specifically. The artificial hormones in birth control pills can trigger change in the gut microbiota and have a negative impact on gut permeability, which can both lead to Crohn’s disease.

Mood and mental health

Hormones play a crucial role in our mood and emotions. Changes in hormone levels when taking oral contraceptives can have an impact on a person’s mood and mental health.

Research in recent years, particularly a 2016 study involving over 1 million women in Denmark, have determined a potential link between hormonal birth control methods and depression. Similarly, preliminary research presented by scientists at the annual meeting Radiological Society of North America in 2019 found that women taking birth control pills had smaller volume of the hypothalamus, the part of the brain that produces hormones and regulates essential bodily functions including sleep cycles, appetite, sex drive, and heart rate. This smaller hypothalamic volume also showed a strong correlation with depression symptoms.

More research is clearly needed on hormonal birth control’s impact on the brain and mental health, but research completed so far is telling.


Oral birth control pills have been the leading choice of contraception method for millions of American women since their introduction to the market, mainly due to their convenience and the multiple health benefits they bring to the table. Despite these benefits, they can still cause a number of serious side effects that can be dangerous to one’s health if left untreated.

If ever you experience any of the symptoms described above, make sure to inform your doctor. There are many forms of contraceptives available and your doctor should work closely with you to find the option that best suits your lifestyle and needs.

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