Would you rather take one pill per day or give yourself two shots a day?

Yeah, this needle-phobic Fool would pick the pill, too.

Amylin Pharmaceuticals (NASDAQ:AMLN) and Eli Lilly (NYSE:LLY) are fighting an uphill battle as they try to convince diabetics that the benefit from the two-needle-prick regimen of Byetta is worth the effort over popping a single Januvia pill from Merck (NYSE:MRK).

The companies ran a head-to-head trial in which Byetta was shown to lower post-meal glucose levels more than Januvia. Patients on Byetta also ate less, which could cause them to lose weight -- a known, and usually welcomed, side effect of Byetta.

While head-to-head trials are usually the definitive answer on which drug is the best, this trial probably isn't going to change the prescribing habits of doctors all that much because Amylin and Eli Lilly appear to have set it up in a way to ensure Byetta's success. Because Byetta is taken before a meal, it's not surprising that it helped lower post-meal glucose levels. (In fact, the drug shouldn't be taken after a meal because of a risk of low blood sugar levels.) A better test would have been to measure hemoglobin A1c levels, which track the average long-term -- two- to three-month -- level of glucose in the bloodstream.

That's what Novo Nordisk (NYSE:NVO) did when it pitted liraglutide, its once-daily injection that's awaiting a Food and Drug Administration marketing decision, head to head against Byetta. It's also using the same measurement to test liraglutide against Januvia.

While the only people likely to be swayed by this trial are doctors and patients who just read headlines, it probably doesn't matter much for Amylin and Eli Lilly. The companies are working in combination with Alkermes (NASDAQ:ALKS) to make a once-weekly version of Byetta. To the companies' credit, they are using hemoglobin A1c levels as the end point, comparing extended-release Byetta to Januvia, Takeda's Actos, and metformin, the long-genericized version of Bristol-Myers Squibb's (NYSE:BMY) Glucophage. It'll be the results of those head-to-head contests that will determine Amylin's ultimate success.

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Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. Eli Lilly is a selection of the Income Investor newsletter. The Fool has a disclosure policy.