“If a research project is never published it is as if it never happened,” Dr. Lauer said.

So starting next year, the heart institute will require that all research results be reported in a federal database even if no journal will publish them. In addition to turning down smaller studies, it is insisting that the costs of large studies go way down — even if that means sacrificing data by, for example, not gathering lab results on peripheral questions researchers think are interesting.

Though some researchers are unsettled by the new practices, many agree that money was often wasted under the old system. Five small studies cost less than one large one, so the temptation, federal officials acknowledge, has been to stuff the clinical trials portfolio with small studies, especially given the reality of the federal budget. Funds for the National Institutes of Health have fallen by 20 percent in inflation-adjusted dollars since 2006.

“It’s worth understanding how perverse — and that’s the right word — the environment has been for clinical trials,” said Dr. Salim Yusuf, a cardiologist at McMaster University in Ontario.

Dr. Lauer never expected to uncover such a troubled system when he asked for data on the publication — or nonpublication — of heart institute studies. The results shocked him and his colleagues, and after some soul searching they reported their findings in The New England Journal of Medicine. They realized they were airing what some said was the institute’s dirty laundry in a journal that is all but required reading for medical researchers. “We did it anyway,” Dr. Lauer said, explaining that he could hardly criticize others for not publishing and then fail to publish his own results.

Others have also unearthed stunning rates of nonpublication. A Yale study found more than half of studies funded by the National Institutes of Health were not published in the 30 months after they were completed. A group at Duke examining more than 13,000 clinical trials of drugs found most had not reported results by five years after completion, even though the Food and Drug Administration requires reporting by one year after a study’s end. Federally funded studies were less likely to report results than those funded by drug companies.

A new Yale study under review at a medical journal found that a failure to publish afflicts researchers equally in prestigious medical centers and ones that are less well known. “If people really knew what was happening they would be outraged,” said Dr. Nihar Desai, a Yale scientist who has been investigating nonpublication.