You probably know that birth control pills increase women’s risk for blood clots…but did you realize that the danger is twice as high for Pill users who have a particular type of hormonal imbalance as it is for other women? Yet despite this hazard, the Pill is often prescribed as a treatment for this very same hormonal problem.

We’re talking about polycystic ovary syndrome (PCOS), an endocrine disorder that affects an estimated 6% to 15% of premenopausal women. Characterized by higher-than-normal levels of androgens (male hormones), PCOS can lead to menstrual irregularities, infertility, excessive facial and body hair, acne, weight gain and an increased risk for diabetes and heart disease. PCOS also increases a woman’s risk for blood clots by about 50%—yet even so, the standard treatment for PCOS is to take oral contraceptives because they contain female hormones that help control the symptoms of the disorder.

Huge new study: Researchers from the FDA and various US and Canadian universities culled data from more than 100 managed-care health insurance plans to find 43,506 women between the ages of 18 and 46 who had PCOS and were taking oral contraceptives, then compared them with 43,506 other women who were also using oral contraceptives but who did not have PCOS. Remarkably, to make the comparison as valid as it could possibly be, the researchers matched each PCOS patient with another woman who had similar comorbidities (additional diseases or disorders), such as obesity or high cholesterol, or who was on similar medications.

The databases were then mined again to look for evidence (such as diagnostic codes or the use of clot-dissolving drugs) showing that the women were treated for a blood clot in a vein, a condition called venous thromboembolism. Usually such clots form in the deep veins of the legs—but if a clot breaks off and travels to the heart, lungs or brain, it can be life-threatening.

Worrisome findings: PCOS patients taking oral contraceptives were more than twice as likely to have a venous thromboembolism as Pill users who did not have PCOS. Granted, such blood clots were uncommon in both groups—over a year’s time, they were diagnosed in about 24 out of every 10,000 Pill-using PCOS patients, versus 11 out of every 10,000 Pill users who did not have PCOS. Still, given that blood clots are potential killers, the increased risk is definitely something that PCOS patients and their doctors need to consider.

If you have PCOS: Certain brands of oral contraceptives present a greater risk for blood clots than others, depending on the particular hormones in the pills. For instance, recent research revealed that birth control pills containing a synthetic form of progesterone known as drospirenone may create up to three times as much risk for blood clots as pills containing other types of progesterone…and we’ve known for a while that pills containing desogestrel also carry an increased risk. To learn which brands are riskiest and which are safest, read our article “The Most Dangerous Birth Control Pills.” Then talk to your doctor to determine which particular type of oral contraceptive—if any—is appropriate for you.