Under gray skies and flanked by Vice President Dick Cheney and Gov. Timothy M. Kaine, the monarch walked along a tourist village of primitive, thatch-roofed buildings.
Cheney noted the queen's last visit to Jamestown, 50 years ago for the 350th anniversary commemoration of its founding.
"Half a century has done nothing to diminish the respect and affection this country holds for you. We receive you again today in that same spirit," Cheney told the queen in a welcoming speech.
The queen did not speak.
She was also greeted by retired Supreme Court Justice Sandra Day O'Connor, who noted the historical ties between the two countries long after America had fought a war to win its independence.
Together, O'Connor said, the two nations had prevailed in two world wars and the Cold War in the 20th century. And the United States had prospered as a free land under laws borrowed from Britain.
"These settlers used these legal tools in forming their community. The establishment of the rule of law derived from Great Britain is the great and lasting achievement we celebrate today," O'Connor said.
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She also noted the stain of slavery got its start in America in Jamestown, where the first Africans arrived in 1619 and that the United States had only begun its long struggle for racial equality when the queen last toured Jamestown.
"Nineteen fifty-seven marked the year that the governor of Arkansas attempted to prevent African-American students from attending Little Rock Central High School," O'Connor said.
Since the queen's last visit there 50 years ago, Jamestown has literally been rediscovered, reports CBS News correspondent Mark Phillips.
The queen toured an archaeological dig taking place at a site archeologists thought was lost in the river mud: the actual foundations and thousands of artifacts from the original settlement in 1607, 13 years before the Pilgrims at Plymouth Rock.
"It's the first act, scene one of the American dream," says Bill Kelso, Jamestown's chief archeologist.
Large crowds waited amid tight security to see the queen, lining her path through Jamestown Settlement.
Carol Rideout of Williamsburg woke long before dawn and headed out to Jamestown Settlement, where she and several hundred others waiting to see Queen Elizabeth II were pleasantly surprised.
2Rather than being kept at a distance from the replica of the three-sided original Jamestown fortress, they were allowed inside for a good view of the monarch.
"I got lucky. Everyone in the world knows Queen Elizabeth II. She's come so far and I just wanted to see her," said Rideout, a retired scientist.
The queen toured a facsimile of the armory believed to have been in the original settlement in the 1600s. Fred Scholpp, a costumed interpreter, showed the queen the sort of weapons it might have contained, including a 17th-century breastplate. She touched it with a gloved hand and smiled.
She also walked to docks on the James River nearby, where replicas of the three sailing ships on which the settlers arrived in 1607 and a cannon was fired from one of the ships in tribute to her.
The queen, Cheney and Kaine will attend a lunch in Williamsburg, then visit the College of William and Mary before the royal couple departs for Louisville, Ky., and Saturday's Kentucky Derby. Next week she visits President Bush in Washington.
On Thursday in Richmond, the queen addressed the General Assembly, lauding social changes in Virginia since her 1957 visit when the anniversary was an all-white affair and the state was in open defiance of a 1954 Supreme Court order to desegregate public schools.