One of the largest studies done to determine whether fertility drugs cause ovarian cancer found that there is "no convincing association" between the two. The New York Times reports:
[T]he researchers followed 54,362 women who had been referred to Denmark's fertility clinics between 1963 and 1998. They gathered information about the women from Denmark's birth, cancer and hospital discharge registries, seeking more detailed information on medications from individual medical records of a subgroup of 1,241 of the women.Among the 54,362 infertile patients followed for an average of 15 years, there were 156 cases of ovarian cancer. The average age of the women by the end of the study was 47.
Medical records were used to analyze the relative incidence of ovarian cancer in women who had taken either gonadotropins, clomifene citrate, human chorionic gonadotropin (hCG) or gonadotropin-releasing hormone, compared with ovarian cancer rates of women who had not taken each of the individual drugs (but may have been treated with one of the other medications).
After adjusting for risk factors, the researchers concluded there was no increase in ovarian cancer risk associated with the drugs, nor was there an increased risk for women who underwent 10 or more cycles of treatment or for women who never became pregnant despite treatment.
This should be somewhat comforting, although the researchers also say this doesn't mean there's absolutely no link. Dr. Allan Jensen, the first author of the paper, said that "over all these data provide further evidence that fertility drugs do not increase the risk of ovarian cancer to any great extent," but also adds that "you should always balance a possible small increase in ovarian cancer risk with the physical and psychological benefits of pregnancy made possible only by use of these drugs."
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They always say that, though; you can't prove a negative etc.