A panel reviewed the evidence and concluded that the "benefits of all combined hormonal contraceptives (CHCs) continue to outweigh risks," the EU watchdog said, using the medical term for contraceptive pills.
"There is no reason for women who have been using CHCs without any problem to stop taking them on the basis of this review."
In January, France asked the EMA to modify prescription guidelines for so-called third- and fourth-generation of the pill, which were introduced in the 1990s and in the last decade respectively.
A Danish study in 2011 found that women who used later generations of the pill ran twice the risk of developing blood clots, known as venous thromboembolism (VTE), compared to those who used older-generation drugs.
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Compared with non-users of the Pill, the risk of a clot was three to six times higher. A VTE can be dangerous as clots formed in the veins can break up and be transported to the heart or lungs.
In absolute terms, though, the risk is low, experts have said.
"There are small differences between the CHCs depending on the type of progestogen they contain," it added.