It's one thing to get beaten in a head-to-head clinical trial by a rival drug, like Johnson & Johnson (NYSE:JNJ) did to Amgen (NASDAQ:AMGN) and Wyeth (NYSE:WYE) last week. It's another to get trounced by alternative medicine.

But that's what happened to Wyeth this week, as researchers announced results of a clinical trial pitting Effexor against acupuncture to see which could relieve hot flashes in women after breast cancer treatment. In the small study (47 women participated), acupuncture was just as effective as Effexor in getting rid of the symptoms, but its effect lasted for 15 weeks after treatment, compared to just two weeks for Effexor. There were also fewer side effects associated with the acupuncture treatment than with Effexor. That's got to sting a little. (Sorry.)

Of course, there's a bit of a caveat here. In a "normal" study, the patients don't know whether they're receiving the drug or a placebo. In this one, well, it's kind of hard to disguise the fact that they're receiving acupuncture. Still, the results are impressive.

Nonetheless, the findings shouldn't hurt Wyeth's revenue too much. Effexor sales mostly stem from patients treating depression, not hot flashes. And besides, I imagine that very few doctors will send their patients out to the acupuncturist, rather than writing a prescription for Effexor, GlaxoSmithKline's (NYSE:GSK) Paxil, or Eli Lilly's (NYSE:LLY) Prozac, all anti-depressants used to treat hot flashes in post-breast cancer women. (More traditional hormone therapy could raise the risk of the cancer returning.) That's just not the way doctors think, positive clinical trial or not.

Wyeth also has bigger problems than getting beat in a head-to-head trial by a bunch of needles. Effexor XR -- its extended-release drug -- will eventually face generic competition, so Wyeth is desperately trying to switch patients to its me-too drug, Pristiq. Add to that Teva Pharmaceuticals' (NASDAQ:TEVA) attempt to stab Wyeth in the heart by launching a generic version of its heartburn medication, Protonix, and those little needles look small by comparison.

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Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. The Fool has a disclosure policy.