As Congress debates immigration reform to allow more highly-skilled workers to come to the U.S., the irony is that it is chasing away a generation of young American scientists by starving them of billions of dollars in funding for important medical research.

Stephanie Zerwas, a University of North Carolina researcher hoping to find the genes that place young girls at risk for developing devastating eating disorders, is one of them.

Last year, she sent a grant proposal to the National Institutes of Health for her first independent investigation, a career milestone for young scientists. She was thrilled to learn in January that her project had been green-lighted by a rigorous peer review process that approves roughly one in ten proposals.

"They said, 'Great. This is good science. This is going to have a big impact on the field and on patients'," she said. "I don't think people realize just how difficult the grant writing process is. It's almost like winning the lottery when you get a grant marked for funding. "

But that lottery ticket may never pay off. Thanks to this year's doomsday budget deal between Congress and the White House known as thesequester, Zerwas is one of about 700 NIH research applicants whose projects have been frozen.

Unless a new budget deal is struck, many of them will likely never see their projects get off the ground.

Sequester cuts in medical research funding could end up widening the federal deficit the cuts were designed to contain in the first place. As an aging population raises the cost of treating diseases like diabetes, heart disease and Alzheimer's, slowing the pace of research will delay the discovery of cures and treatments that might slow the rise in health care costs.

Longer-term, ongoing projects are also threatened as they've been forced to scale back.

"Which of those (frozen research) grants might have been the next breakthrough in cancer research?" said NIH Director Francis Collins. "Which of those grants was going to support the career of a young scientist who will now basically give up and say I'd better do something else or move to another country? We'll never know. They're gone."

Like Zerwas, 37, many of those battling for a shrinking pool of research funding are young scientists trying to grab the first rung of a lifelong career. But a decade of federal research funding cuts is now sidelining the careers of the many of America's next generation of most highly skilled workers.

Those who succeed in launching their careers have to wait longer. The average age of a researcher winning their first independent NIH grant last year was 44, up from 36 in 1980.

The funding drought has forced many to reconsider their career choice. Some are looking for—and finding—better opportunities outside the U.S.

Michael Hendricks, 40, is a neuroscientist studying the basic functioning of the nervous system in roundworms. He's hoping his work will provide a research foundation for advances in treat of human diseases like Alzheimer's or Parkinson's.

With funding drying up in the U.S., he's leaving a job at Harvard University to set up his own lab at a large research university in Canada.

"There's a diminishing sense that the U.S. is the place to be," he said. "There are more opportunities in China or in Singapore or increasingly in the Middle East where there are these brand new research institutions where funding is not an issue and where they have facilities that are on par with the best in the U.S."

(Read More: Stories of Struggle And Creativity As Sequestration Cuts Hit Home)

You don't have to have a Ph.D. to see why young American scientists are leaving the country.

Even before this year's budget sequester, the odds of winning the research grant lottery have been getting longer.

NIH funding had already been cut by 17 percent over the past decade. Adjusted for inflation, that puts overall funding at levels not seen since 1999. Those cuts have reduced the odds of getting funded from one in three to as low as one in ten.

As the U.S. has been cutting back, China and India are boosting funding by 20 percent a year; Brazil, South Korea and Japan by 10 percent, Germany by 8 percent, said Collins.

"It seems what we, alone, have adopted a strategy of cutting just at the time where everyone else has looked at our success story – and the way in which this kind of research stimulates the economy," he said. "We seem to have forgotten that."

Ironically, the immigration barriers that prevent foreign students from pursuing research careers in the U.S. don't prevent them from studying at federally-funded research universities and building their technical skills here. If they're denied permission to stay in the U.S., the economic return on the U.S. government's investment in their training leaves with them.

"People like me going to Canada is small scale stuff," said Hendricks. "But the many tens of thousands of foreign Ph.D. students and post docs—who were trained with U.S. taxpayer money and many of whom would probably prefer to stay in the U.S.—will leave to pursue better career opportunities in Asia and Europe."