The Republican majority in the House and comeback in the Senate after Tuesday's elections could bring changes to the nation's health research funding, experts say.

The GOP agenda for 2010, known as the Pledge to America, calls for federal spending to be cut to 2008 levels.

If this happens, the National Institutes of Health could see its budget dip from 31.3 billion — the requested budget of 2011 — to 28.5 billion, a loss of 9.1 percent. About 97 percent of U.S. government health research funding comes from the NIH.

This would mean government and university researchers across the country could see their funding cut, said Stacie Propst, vice president of science policy and outreach at Research America, a nonprofit organization in Virginia that advocates making health research a national priority.

"It wouldn’t just be that the [NIH] itself would lose money, it would actually be the states and their universities and their health care industry partners — those people would lose the money," she said.

Young researchers are likely to be most affected, Propst said. "The first scientists to suffer when research funds are squeezed are always the newer investigators," who typically seek funding from the NIH, she said. "If there aren’t additional funds available, those are the people that get cut out of the system first."

However, the Pledge to America does not specifically say where the funding cuts will come from except that they won't be from military agencies, said Patrick Clemins, the director of the research and development budget and policy program at the American Association for the Advancement of Science.

In fact, the NIH might avoid the brunt of the cuts, because historically, Republicans tend to favor health funding, he said. NIH funding doubled between 1999 and 2003, and the increase started under a Republican Congress.

"If you look at it that way, there's a chance — I would say a good chance — the NIH could be spared some or all of those cutbacks."

And while many government agencies are likely to see budget loses in the next year or two, these agencies, including the NIH, "will find money in their budget to drive their highest priority initiatives, even during tough fiscal times," Clemins said.

A big loser from the recent election results could be embryonic stem cell research.

A federal judge issued an injunction in August that restricted all federal funds for embryonic stem cell research, stating these funds were in violation of the Dickey-Wicker Amendment. This amendment essentially prohibits government funding on research that involves destruction of human embryos.

Backers of embryonic stem cell research say the injunction blocks funding for research using cell lines already in existence — which don't require more embryos to be harmed — and had hoped this amendment could be removed, or new legislation passed to override it. Now, some are skeptical this will happen.

"I think funding for embryonic stem cell research is in seriously jeopardy because of the election," said Arthur Caplan, director of the center for bioethics at the University of Pennsylvania. "The election of a Republican House and a more conservative Senate makes it unlikely that the legislation is going to get changed," he said.

The best bet for supporters of embryonic stem cell research would be to get legislation passed in the "lame duck" session of Congress, before the newly elected officials take their seats, Propst said.

If that doesn't happen, Propst said it was not likely a stem cell funding bill would get through Congress in the next term. But she noted a number of Republicans have been supportive of stem cell research in the past.

All the red tape surrounding this type of research may take its toll in terms of the number of scientists interested in the field, Caplan said.

"Younger scientists are not wanting to get into this area that's likely to be tangled up in legislative and court disputes for the next few years…that’s not a good way to build a career," he said.

This story was provided by MyHealthNewsDaily, a sister site to LiveScience.