This ruling came as quite a shock to scientists because for more than a year, they've been receiving a steady flow of federal funding, but all of that is now in jeopardy.
Embryonic stem cell researchers say their field is now in a state of turmoil and those who've devoted their lives pushing for stem cell research now have their hopes on hold.
Don Reed's son, Roman, is paralyzed from the waist down.
"Every day of delay is research denied, is a cure denied. People are suffering now. We got to get this political nonsense out of the way," says Reed.
It was just last year when President Barack Obama signed an executive order expanding embryonic stem cell research. Since then, the number of stem cell lines has nearly quadrupled.
But on Monday, U.S. District Judge Royce Lamberth blocked federal funding. He ruled the Obama administration violates the Dickey-Wicker amendment, a law passed annually by Congress that bans federal financing for any research "...in which a human embryo or embryos are destroyed, discarded or knowingly subjected to risk of injury or death."
The Obama administration argued federal money isn't used to destroy embryos, only used after the stem cells are created. Lamberth disagreed and right to life groups are claiming victory.
"We are thrilled with the decision because we believe that life begins at fertilization and so we see an embryo as being a human being," says Cecelia Cody with the California Right to Life Educational Fund.
Alan Trounson is president of the California Institute for Regenerative Medicine, the voter-approved, $3 billion agency that doles out money to research projects throughout the state. He says the federal ruling won't affect their funding practices, but worries scientists will ultimately look for a more steady line of work.
"That's what I think what might happen in this area, the scientists may move because of the difficulty in keeping continuous funding," says Trounson.
The National Institutes of Health and the White House declined to comment on Monday's ruling. They say the justice department is reviewing the decision.
Supporters of embryonic stem cell research are hoping for an appeal.