Comparative medicine, pitting one therapy against another, is coming to a press release near you. In addition to the $1.1 billion in last year's health-care reform bill, there's a requirement to put aside $500 million or more each year to fund head-to-head clinical trials.

Some drug and medical device companies surely will be hurt by the results of the trials, but they can't really be upset by the testing. If their products offer true advantages, the trials would benefit them, and could result in faster uptake of new therapies.

The problem is that the "advantage" is defined by some outside force -- whoever is designing the clinical trial. For some therapies, the measure of success is rather clear. If you're going to compare Pfizer's (NYSE: PFE) Sutent with Bayer and Onyx Pharmaceuticals' (Nasdaq: ONXX) Nexavar in kidney-cancer patients, the one that helps patients live longer is clearly the one you'd like to take. If they perform the same, choose the cheaper one.

But for other comparative trials, the measure of success isn't as clear.

A painful choice
A study published in 2007 showed that inserting stents like those made by Johnson & Johnson (NYSE: JNJ) and Medtronic (NYSE: MDT), along with competitors Boston Scientific (NYSE: BSX) and Abbott Labs (NYSE: ABT), was no better at keeping patients from having heart complications compared with trying cheaper medications first, and then following up with stents if necessary.

All things being equal, the cheaper option -- drugs first, which was all some patients needed -- should win. But all things aren't equal. The stents made the pain go away faster than starting with medication. They also alleviated the need for daily medication, which patients would prefer to avoid if they can.

But how do you put a dollar value on the decrease of pain? At this point, the question is moot: Most insurance companies will cover both options. But as the push for major cost-cutting gets stronger, it's only a matter of time before we'll have to answer that question.

A high-tech example
Robot-assisted surgery is expensive. The daVinci systems sold by Intuitive Surgical (Nasdaq: ISRG) cost $1.4 million, and then there's nearly $2,000 in instruments and accessories for each individual procedure. I'm not sure what a scalpel is going for these days, but I'm guessing it's substantially less.

But the da Vinci system also offers some substantial benefits over traditional surgery for patients that can justify the high instrument cost. You can quantify the financial benefits of some of them, like reduced requirements for blood transfusion  and shorter hospital stays, which lower the risk of infections picked up in the hospital. But there are others, like reduced pain, faster recovery, and the lower chance of impotence after prostatectomies, where a dollar amount can't be assigned easily.

If insurance groups or the Centers for Medicare and Medicaid Services (CMS) decide the quantifiable benefits favor traditional surgery over the robot-assisted kind, and they disregard the harder-to-quantify benefit of less pain, Intuitive Surgical's sales are sure to suffer.

A miserable decision for investors
The health-care reform that passed could more aptly be called health-insurance reform, because the law's ability to control medical costs is fairly limited. It seems to me that another round of changes for the medical community is inevitable. One possibility would be to change how doctors are reimbursed. After all, the spiraling costs can't go on forever.

When that change might occur -- if it ever does -- is difficult to know. Assuming you don't want to completely abandon the high-flying sector, the best investors can do is recognize that the risk exists. Identify the unquantifiable benefits of the treatments your companies own, and factor in the risk that some time down the line, payers may not put much value on those benefits.

Pfizer is a Motley Fool Inside Value selection and Intuitive Surgical is a Rule Breakers recommendation. Johnson & Johnson is an Income Investor selection, and Motley Fool Options recommended buying calls on the stock. Try any of our Foolish newsletters today, free for 30 days

Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. The Fool owns shares of and has written puts on Medtronic. Having escaped the death grip of the paper shredder, the Fool's disclosure policy is pain-free.