Think your doctor knows which drug - or surgery or even diagnostic test - works best? Think again. Half the time, there's little if any good evidence comparing one to another. And one of medicine's little secrets is that brand-new drugs don't have to work any better than cheap old ones to be approved for sale.

Now the government has a $1.1 billion down payment to start unraveling that problem, money provided in the economic stimulus package to better determine which test or treatment works best, when and for whom so that patients don't waste time and money on poor choices.

But which ailments go to the top of a very long wish list? And perhaps most important, how to make sure the results get into doctors' and patients' hands but not overly limit what therapies people can choose?

"There's a lot of clamor ... that this is going to deprive people of the choice to basically have every treatment they want. That's based on a false premise," Dr. Harold Sox, past president of the American College of Physicians, told The Associated Press. Last week, Sox was chosen to lead a panel of the prestigious Institute of Medicine to help guide what comparisons the government makes.

"If people had a good explanation of why a test that they wanted was more likely to hurt them than to help them, they might of their free choice say, 'You know, I was clearly wrong. I shouldn't want that test and now I don't.'"

At issue is what's called "comparative effectiveness." Should you have open-heart bypass surgery or far less invasive stents to open severely clogged heart arteries? Which of two hot treatments best prevents stroke from a clogged neck artery, surgically rooting out the clog or pushing it aside with a stent?

Does arthroscopic surgery work any better than painkillers for knee arthritis? Of all the competing pills, which is best to start with in treating Type 2 diabetes or high blood pressure? Is there really any difference between Prevacid and Prilosec for heartburn, or between Fosamax and hormone treatments for bone-weakening osteoporosis?

Those winners-and-losers questions drive fierce opposition to comparison effectiveness research from drug makers and others who have a financial stake in the outcome and fear that insurers will use the results to make coverage decisions. Back surgeons once lobbied to kill the federal Agency for Healthcare Research and Quality after it found "insufficient evidence" supporting certain spine operations - not that they didn't work, just that more evidence was needed.

The result: The nation has a scattershot method for determining best medicine. The little-known AHRQ spends about $30 million a year reviewing evidence of select tests and treatments. The National Institutes of Health occasionally compares contested therapies in expensive, years-long studies involving thousands of patients, like the stroke trial now under way.

So an extra $1.1 billion for the government to start spending on such comparisons this year marks a huge jump. By June's end, the Institute of Medicine panel will provide a priority list of up to 50 vexing medical questions to help the feds determine where to start.

Don't expect easy answers. Federal scientists are acutely aware that many of today's studies don't account for wide variations in responses to treatments by minorities or other subgroups.

"We have not yet seen a report or an assessment that says, 'Option A thumbs up, Option B forget it,'" says AHRQ Director Dr. Carolyn Clancy. The goal is "to figure out what's the right choice for me."

"Medical decision-making is rarely black-and-white," adds the NIH's heart chief Dr. Elizabeth Nabel. "We see certainly helping to provide additional evidence that really guides physicians and individuals in sorting through the shades of gray."

The bypass-versus-stent question for severe heart disease is a good example. Last week's New England Journal of Medicine published a comparison suggesting bypass recipients fare slightly better. But Nabel notes that in fact the study found tradeoffs that mean people may legitimately choose the easier recovery of a stent.

A bigger question is how to ensure that patients get the opportunity to consider such findings. AHRQ has begun translating its jargon-filled comparisons into easy-to-understand consumer brochures.

But the most-used comparative effectiveness research may come from a unique program in Oregon called the "Drug Effectiveness Review Project" that evaluates the evidence behind competing drugs.

One example: Two years before the painkiller Vioxx was pulled off the market because of heart side effects, the project declared it riskier than its equally effective cousins, says project director Mark Gibson at Oregon Health and Science University.

The reports don't weigh drug costs but they are used primarily by the Medicaid directors of 14 states in coverage decisions. A wider audience sees them thanks to the influential Consumers Union, which does add price to evaluations done by both the Oregon project and AHRQ to create its free Web-based "Best Buy Drugs" guides.

On the Net:
AHRQ: http://effectivehealthcare.ahrq.gov
Oregon project: http://www.ohsu.edu/drugeffectiveness/