Side Effects and Risks
The documented side effects of hormonal birth control — nutrient depletion, mood changes, blood clots, and more
Hormonal birth control is generally presented as safe and well-tolerated. For many women it is. But "generally safe" doesn't mean "no side effects," and the list of documented effects goes well beyond what most prescribers discuss. This isn't about fear-mongering -- it's about knowing what to watch for and what the research actually shows.
Every woman responds differently. Some take the pill for years with no noticeable issues. Others experience significant changes in mood, energy, libido, or health. Both experiences are valid.
Nutrient Depletion
Hormonal birth control has been shown to deplete several key nutrients [2]:
- B vitamins: B6, B12, and folate are consistently depleted in oral contraceptive users. This is particularly concerning for folate, since women often go straight from the pill to pregnancy, when folate demand is highest for preventing neural tube defects [2].
- Magnesium: Already the most common mineral deficiency in developed countries, and the pill makes it worse. Magnesium is involved in over 300 enzymatic reactions including mood regulation, sleep, and muscle function. (See: Magnesium)
- Zinc: Essential for immune function, thyroid health, and hormone production. The pill lowers zinc while raising copper levels, potentially disrupting the zinc-to-copper ratio [2]. (See: Zinc)
- Selenium: Important for thyroid function and antioxidant defense.
- Vitamins C and E: Both are depleted, reducing antioxidant capacity [2].
If you're on hormonal birth control, a quality B-complex, magnesium, and zinc supplement may help offset some of these depletions.
Depression and Mood Changes
The largest study on this topic is the landmark Skovlund et al. (2016) study published in JAMA Psychiatry [1]. Researchers followed over one million Danish women aged 15-34 for an average of 6.4 years and found:
- Women on combined oral contraceptives had a 23% increased risk of being prescribed antidepressants
- Progestin-only pills carried a 34% increased risk
- The patch showed a 100% increased risk (doubled)
- The hormonal IUD (levonorgestrel) showed a 40% increased risk
- Adolescents (ages 15-19) were hit hardest -- an 80% increased risk of depression with combined pills, and a 120% increased risk with progestin-only pills [1]
These are not small numbers, and this was not a small study. For years, women who reported mood changes on the pill were told it was "in their head." This study confirmed what many women already knew.
Blood Clot Risk
Combined hormonal contraceptives (those containing synthetic estrogen) increase the risk of venous thromboembolism (VTE) -- blood clots in the deep veins (DVT) or lungs (pulmonary embolism) [3]:
- The overall risk increases approximately 3 to 4 times compared to non-users
- Newer progestins (desogestrel, gestodene, drospirenone) carry roughly double the clot risk of older progestins like levonorgestrel [3]
- Risk is highest in the first year of use and in women who smoke, are overweight, or have a family history of clotting disorders
The absolute risk is still relatively low for healthy young women -- roughly 3-9 per 10,000 women per year on the pill versus 1-5 per 10,000 in non-users [3]. But blood clots can be life-threatening, and many women aren't adequately screened for risk factors before being prescribed hormonal contraception.
Reduced Libido
The pill increases sex hormone-binding globulin (SHBG), which binds free testosterone. Since testosterone is a primary driver of libido in both men and women, this can significantly reduce sexual desire. Some research suggests SHBG levels may remain elevated even after discontinuing the pill, potentially affecting libido long after stopping.
Altered Partner Selection
This one is fascinating and under-discussed. Research suggests that hormonal contraception may alter women's mate preferences [4]. Naturally cycling women tend to prefer markers of genetic dissimilarity (detected partly through body odor/MHC genes), which is thought to promote immune diversity in offspring. Women on hormonal BC show shifted preferences -- sometimes toward more genetically similar partners [4]. Some researchers have speculated this could contribute to relationship dissatisfaction after discontinuing the pill, though this remains an area of active research.
Other Documented Effects
- Gut microbiome disruption: Hormonal contraceptives are associated with changes in gut microbial composition and increased intestinal permeability, with some studies linking long-term use to increased risk of inflammatory bowel disease
- Cancer risk shifts: Hormonal BC modestly increases the risk of breast cancer and cervical cancer while decreasing the risk of ovarian and endometrial cancer -- a trade-off that's rarely discussed as such
- Inflammatory effects: The pill increases C-reactive protein (CRP), a marker of systemic inflammation
- Thyroid effects: By increasing thyroid-binding globulin, the pill can mask thyroid issues or alter thyroid hormone availability
Evidence Review
The Skovlund et al. (2016) study in JAMA Psychiatry remains the most robust evidence linking hormonal contraception to depression [1]. Its strengths -- prospective design, national registry data, over one million participants, and adjustment for confounders -- make it difficult to dismiss. The dose-response relationship (higher risk with higher-dose progestins) and age-related vulnerability (adolescents most affected) add biological plausibility. Critics note that antidepressant prescriptions are an imperfect proxy for depression, and that the absolute risk increase is modest. However, the consistency of findings across different formulations and delivery methods supports a real pharmacological effect.
Palmery et al. (2013) reviewed the mechanisms by which oral contraceptives deplete micronutrients, including altered absorption, increased metabolic turnover, and changes in tissue distribution [2]. The depletion of folate is particularly well-established and has led some countries to recommend folate supplementation for all women of reproductive age on oral contraceptives. The clinical significance of other depletions (B6, B12, zinc, magnesium, selenium, vitamins C and E) varies by individual diet and baseline status, but the pattern is consistent across studies.
Vinogradova et al. (2015) conducted a large nested case-control study using UK primary care data, confirming a 3-4 fold increased risk of VTE with combined oral contraceptive use [3]. Their finding that newer-generation progestins carry higher clot risk than older formulations contradicted marketing claims and has influenced prescribing guidelines. The absolute risk remains low for healthy non-smoking women under 35, but individual risk assessment before prescribing remains important.
Roberts et al. (2014) reviewed evidence that hormonal contraception alters mate preferences, particularly regarding MHC-dissimilarity preferences in mate choice [4]. While the evidence is suggestive rather than conclusive, several independent studies have found preference shifts. The evolutionary and relationship implications remain speculative, but the finding that a medication can alter something as fundamental as partner attraction underscores how far-reaching hormonal effects can be.
Where the evidence stands: The side effects listed here are documented in peer-reviewed research, not fringe claims. That doesn't mean every woman will experience them, and it doesn't mean hormonal birth control is "bad." It means these are real trade-offs that deserve to be part of the conversation between a woman and her doctor -- not dismissed or minimized. Informed consent requires knowing both the benefits and the risks.
References
- Association of hormonal contraception with depressionSkovlund CW, Morch LS, Kessing LV, Lidegaard O. JAMA Psychiatry, 2016. PubMed 27680324 →
- Oral contraceptives and changes in nutritional requirementsPalmery M, Saraceno A, Vaiarelli A, Carlomagno G. European Review for Medical and Pharmacological Sciences, 2013. PubMed 23852908 →
- Risk of venous thromboembolism from use of oral contraceptives containing different progestogens and oestrogen dosesVinogradova Y, Coupland C, Hippisley-Cox J. BMJ, 2015. PubMed 25439778 →
- Does the contraceptive pill alter mate choice in humans?Roberts SC, Little AC, Burriss RP, et al.. Trends in Ecology & Evolution, 2014. PubMed 24011750 →
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