Pope John Paul II urged Mr. Bush in their first meeting to bar creation of human embryos for medical research, saying that America has a moral responsibility to reject actions that "devalue and violate human life."
The president and pontiff met for a closed-door discussion at the papal summer residence south of Rome.
In a statement after the meeting, the pope lamented "evils such as euthanasia, infanticide, and, most recently, proposals for the creation for research purposes of human embryos destined to destruction in the process," referring to a recent study in Virginia where an embryo was, for the first time, created specifically for research purposes.
"A free and virtuous society, which America aspires to be, must reject practices that devalue and violate human life at any stage from conception to natural death," the pope said.
Scientists believe research using stem cells could unlock the cures for many diseases, including Alzheimer's, Parkinson's, diabetes and spinal cord injuries. However, abortion rights opponents say harvesting the stem cells requires the death of an embryo, which many regard as human life.
Mr. Bush has promised a decision soon on federal funding for the research, but aides say no announcement is imminent.
After meeting the pope, Mr. Bush told reporters he was spending a good deal of time trying to fully understand the issue.
"It is an issue that, on the one hand, deals with so much hope, hope that perhaps through research and development we'll be able to save lives," Mr. Bush said during a joint news conference with Italian Prime Minister Silvio Berlusconi.
"It's also an issue that has got serious moral implications, and our nation must think carefully before we proceed," he said. "And therefore my process has been, frankly, unusually deliberative for my administration. I'm taking my time."
By speaking out specifically against embryo stem-cell research he appeared to leave some maneuvering room for Mr. Bush, a Methodist, who has been courting Catholics a large and potent swing group in the U.S. electorate.
In contrast to the specific objection John Paul raised, embryos involved in the research that Mr. Bush is considering are not created for scientific study but are taken from fertility clinic surpluses that would otherwise be discarded.
The Roman Catholic hierarchy is staunchly opposed to stem cell studies. But even some of the president's conservative Republican allies support the research. They believe it could save or extend the lives of disease victims like former President Ronald Reagan, who suffers rom Alzheimer's.
Mr. Bush has spoken of how much he looked forward to meeting the frail 81-year-old John Paul, whose 23-year pontificate has spanned five American presidencies.
Mr. Bush has said the issue was "beyond politics."
"I, frankly, do not care what the political polls say. I do care about the opinions of people, particularly someone as profound as the Holy Father," Mr. Bush said. "Of course I'll take that point of view into consideration as I make up my mind on a very difficult issue confronting the United States of America."
Mr. Bush thanked the pope for reminding Americans that their prosperity "must be matched with compassion and moral purpose."
Always to all you have carried the gospel of life, which welcomes the stranger and protects the weak and the innocent," said Mr. Bush. "Every nation including my own benefits from hearing and heeding this message of conscience."
Before their statements, Mr. Bush gave John Paul a book of poetry. They stood together on the balcony of the pope's library, overlooking the clear blue waters of Lake Albano, and Mr. Bush commented: "On a hot day it looks like a place one would go swimming."
The president returns to the United States Tuesday night after visiting with U.S. troops in Kosovo.
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