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“This injunction blocks important research on how to unlock the enormous potential of human embryonic stem cells,” he said.

The decision leaves the Obama administration with a choice: whether to continue to fight the lawsuit, despite the strong likelihood of success, or take advantage of the strong Democratic majorities in both houses of Congress, likely to be thinned in the upcoming midterm elections, to repeal the Dickey-Wicker Amendment.

“They may appeal this, but I wouldn’t be surprised if they try to go back through Congress during the lame-duck session, because the composition of Congress may change significantly after November,” Dr. Stevens said.

First introduced in 1995 and signed by President Clinton, the Dickey-Wicker Amendment has been included every year since then in the appropriations bills funding the Health and Human Services Department. It was named for its two Republican House sponsors, Reps. Jay Dickey of Arkansas, who is no longer in Congress, and Roger Wicker of Mississippi, who now serves in the Senate.

One irony is that the case was originally dismissed by the same judge after he found that the two adult stem cell researchers listed as plaintiffs — James Sherley of the Boston Biomedical Research Institute and Theresa Deisher of AVM Biotechnology — lacked standing, or the legal right to bring a case.

The U.S. Circuit Court of Appeals for the District of Columbia reversed Judge Lamberth in June, stating that the two researchers could bring a case on the basis that their work could be hurt by the added competition for federal scientific funds.

Judge Lamberth’s ruling Monday was not a decision on the merits of the researchers’ lawsuit, which will be tried later. Rather, it blocks the Obama administration’s policy from taking effect while the case is being tried, something judges do only when they think the plaintiffs have a good chance of winning their case.

In his signing ceremony, Mr. Obama said that embryonic stem cell research had the potential for medical breakthroughs that could lead to cures for devastating illnesses and injuries. He said the ethical dilemma should be resolved in favor of helping the living.

“As a person of faith, I believe we are called to care for each other and work to ease human suffering,” Mr. Obama said at the time. “I believe we have been given the capacity and will to pursue this research — and the humanity and conscience to do so responsibly.”

A Justice Department spokeswoman said the administration was reviewing the decision late Monday afternoon.

Mr. Bush had limited stem cell research to the roughly 20 then-existing lines of embryonic cells. The Obama signing order permitted research on cells from any line of embryos that were otherwise scheduled for disposal.