However, long-term studies (the NIH-sponsored Women's Health Initiative, or WHI) of women receiving combined hormone therapy with estrogen and progesterone showed an increased risk for heart attack, stroke, and breast cancer when compared with women who did not receive HT. Studies with estrogen therapy alone showed that estrogen was associated with an increased risk for stroke, but not for heart attack or breast cancer. Estrogen therapy alone, however, is associated with an increased risk of developing endometrial cancer (cancer of the lining of the uterus).

More recent medical research has suggested that in younger postmenopausal women, hormone therapy may not have these same risks as in the older postmenopausal women who participated in the WHI studies, and research is ongoing to determine the risks and benefits of hormone therapy in younger postmenopausal women and women around the age of menopause.

The decision regarding hormone therapy, therefore, should be individualized for each woman, recognizing her medical history, the severity of the symptoms, and the potential risks and benefits of hormone administration.

A number of non-hormonal prescription medications and alternative treatments have also been used for the treatment of hot flashes (see below).

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