(FORTUNE Magazine) – When Leslie Wallace began having symptoms of menopause five years ago, her doctor prescribed Prempro, a combination of the hormones estrogen and progestin (synthetic progesterone). She wanted relief from hot flashes and night sweats, and she liked what the doctor said about estrogen's protecting against heart disease. It seemed a good idea to have help against the No. 1 cause of death for women. "There were all these advantages and minimal risks," says Wallace, a 53-year-old nurse.

Today the thinking about taking hormones during and after menopause isn't so clear-cut. Not that hormones are bad; they're just not the wonder drugs we thought. Some studies indicate that estrogen does not, in fact, ward off cardiovascular disease; if a woman already has it, hormones may make it worse. Evidence from several large clinical trials of estrogen and menopausal women prompted the American Heart Association in 2001 to revise its guidelines and recommend that women not take estrogen solely to prevent heart attacks and stroke. For women who already have heart disease, the AHA advised against any kind of hormone replacement therapy.

Estrogen is ideal for alleviating hot flashes, slowing bone loss, and perhaps even helping women feel younger. Yet along with the benefits come risks, including increased susceptibility to blood clots, gallstones, and worst of all, breast cancer. As long as estrogen was thought to prevent heart disease, even that risk seemed worthwhile: One in two women will eventually die of heart disease or stroke, vs. one in 25 of breast cancer. But now many doctors tell women to take estrogen (and progestin if they still have a uterus) to alleviate menopausal symptoms, then taper off and stop. "We have very good evidence supporting the effectiveness of other drugs like Fosamax for preventing bone loss and fractures," says Deborah Grady, a professor of medicine and epidemiology at the University of California at San Francisco. "The side effects are things like heartburn--not a threefold increase in blood clots and a 36% increase in breast cancer [as with estrogen]."

Drug companies are eager to offer alternatives to hormone replacement therapy. Pfizer, Eli Lilly, and others are working on selective estrogen-receptor modulators (SERMs), hormones that in theory offer some of the positive effects of estrogen and none of the negative ones. SERMs behave like estrogen in certain tissues of the body--and like estrogen blockers in others. Tamoxifen, a SERM that's been on the market for years as Nolvadex by AstraZeneca, reduces the risk of breast cancer. Raloxifene, introduced three years ago by Lilly as Evista, has estrogen-like effects on a woman's bones without negative effects on her breasts. Neither drug relieves hot flashes, though. More powerful SERMs like Pfizer's lasofoxifene--which seems to both lower blood pressure and prevent bone loss in healthy menopausal women--are still being developed and won't be available for several years.

Women concerned about estrogen's side effects sometimes turn to nondrug alternatives. Black cohosh, used by Native Americans and Europeans in the 19th century to treat gynecological disorders, is sold in over-the-counter herbal supplements like RemiFemin. Hormones derived from plant products--including soy, Chinese yams, and peanuts--are chemically similar to estrogen and progesterone in the body. Significantly, though, scientists refer to these plant estrogens as "weak estrogens" because they lack the punch of the real thing. Then there are soy food products, like tofu, which contain compounds called isoflavones that mimic natural estrogen. Asian women consume lots of soy; possibly as a result, only 14% to 18% complain of menopausal symptoms, vs. 70% to 80% of U.S. women. Some studies say eating 20 to 40 grams of soy a day can cut the incidence of hot flashes. But the research is not conclusive. Like so much else with menopause, it is a work in progress.

--MELANIE WARNER