WASHINGTON — A decade after the government began trying to ensure that prescription drugs used to treat children work and are safe, doctors still have scant information to guide them when they administer many medications to kids.

Although federal regulators have enticed or forced pharmaceutical companies to conduct hundreds of studies that have produced vital results about more than 200 drugs, perhaps two-thirds of the thousands of medications given to children remain untested on them.

“Are there children dying because of this? I don’t know. Are there children being less effectively treated because of this? Probably yes. But I can’t tell you because I don’t know,” a spokesman for the American Academy of Pediatrics, Richard Gorman, said “That’s the problem: We don’t know what we don’t know.”

What researchers have discovered has been disturbing. A highly effective adult migraine drug, for example, turned out to be worthless in children while sometimes causing serious side effects, including strokes. An asthma inhaler could inhibit growth. A narcotic patch routinely used to relieve pain, could cause fatal overdoses. Doctors were giving far too little of a medicine used to prevent seizures.

The alarming gap in medical knowledge is the legacy of many factors. The testing of drugs in children was shunned for decades as unnecessary and unethical; Congress and the pharmaceutical industry failed to provide adequate funding; and conducting medical experiments on children is difficult.

“We’re chipping away at the problem, but we still have a long way to go,” Mr. Gorman said. “It’s like trying to turn an oil tanker: It takes a long time to get it moving in the right direction. And even when it’s moving in the right direction there’s a big ocean it has to get across. There’s still a big ocean of unstudied drugs that we have to sail across before we complete them all.”

The quandary stems from the same dynamics that left over-the-counter pediatric cold remedies on drug store shelves despite little evidence they helped and mounting evidence that they could be dangerous. Drug companies, regulators and researchers long thought doctors could safely extrapolate the results of studies in adults and simply scale down the doses.

“Up to the late 1990s, children were mostly left out of new drug development,” an emeritus professor of pediatrics at the University of Missouri School of Medicine, Ralph Kauffman, said. “It just wasn’t thought necessary.”

At the same time, pharmaceutical developers had little incentive to focus on children.

“Pediatric patients were always the orphans. People didn’t pay enough attention to them. They’re just not a big enough market share,” associate director for the pediatric and maternal health staff at the FDA’s office of new drugs, Lisa Mathis, said.

But researchers started to realize that children react to many drugs in surprising ways.

“Children are different — they are not just small adults,” a professor of pharmacology and pediatrics at the University of Missouri in Kansas City, Gregory Kearns, said. “They are not just fractions of adults.”

In 1997 Congress began to address the problem. The FDA Modernization Act gave the agency a crucial tool — it could offer companies six precious extra months to sell a drug without competition if they studied it in children. The prospect of millions if not billions of dollars of extra sales stimulated a willingness and the necessary infrastructure to do such testing on a wide scale.

Congress renewed FDA’s authority in 2002 with the Best Pharmaceuticals for Children Act, which also established mechanisms for the FDA to work with the National Institutes of Health to start scrutinizing some drugs companies ignored or had no incentive to study because they had already had generic competitors. The legislation called for Congress to appropriate $200 million for the NIH to study the highest-priority medications. And in response to criticism that the pharmaceutical industry was getting a windfall from profitable patent extensions, the legislation established a fund to help finance studies companies would not at the Foundation for the National Institutes of Health, a private nonprofit entity.

“There was a lot of horse-trading going on and the pharmaceutical companies implied they would also step up to the plate,” Mr. Gorman said. “The industry was saying, ‘Yes, we’re making money off this. But we’ll put some of it back into this fund to study drugs being used in children.'”

Advocates pushed for a written commitment from the industry to provide $6 million a year, the American Academy of Pediatrics’ chief lobbyist at the time, Elaine Zining, said. Then-Rep. Billy Tauzin, a Republican of Louisiana, chaired the House committee that negotiated the legislation. “Unfortunately for children, that money never materialized,” Ms. Zining said. Mr. Tauzin subsequently took over as the head of the Pharmaceutical Research and Manufacturers of America (PhARMA).

The foundation has raised just $4.2 million — barely enough to pay half of one study of one drug. Industry representatives said there was never a formal obligation to contribute to the fund. Noting companies were spending tens of millions of dollars sponsoring studies of patented drugs, they blamed the shortfall primarily on the failure of Congress to appropriate the promised money.

“The expectation was that NIH funding would come into play to help conduct those studies,” a spokesman of PhARMA, Alan Goldhammer, said.

Of about 50 drugs that have been deemed high priority, the NIH has managed to launch studies of 14, including Ritalin, lithium, and morphine. But only preliminary steps have been completed.

“It takes time, and it’s complicated,” Mr. Mattison said. “We’ve made substantial progress in terms of identifying drugs that need to be tested and the appropriate testing that we need to do to better understand how to use them in children. But these are very difficult studies to do.”