The queen toured the site in east London for the second time since the British capital was awarded the Olympics in 2005.
Elizabeth viewed the main Olympic Stadium and walked along a section of the 100-meter track area. She was accompanied by Sebastian Coe, a two-time Olympic 1,500-meter champion who heads London's organizing committee.
"We are thrilled to welcome Her Majesty back to show the progress we've made," Coe said. "The skyline in this part of London is being changed forever and the Olympic Park will become a home to world class sport in 2012 and home to a new community afterwards."
The queen got a look at where the royal box will be located in the 80,000-capacity stadium. She also planted the first of 4,000 trees to be put on the park site.
"Planting the tree today is the first step in the creation of a new green space that will reflect the traditions of great British parks and will create a fantastic backdrop for the games," Olympic Delivery Authority chairman John Armitt said.
Elizabeth is expected to open the Olympics in 2012 when she will be celebrating her 60th year as queen.
The visit came three days after London marked the 1,000-day countdown until London's 2012 opening ceremony.
The 1-square-mile Olympic Park also includes the velodrome, aquatics center, basketball arena and main media center. It is next to the athletes' village.
The visit comes amid debate over whether the site should be named Elizabeth Park after the queen. The British Olympic Association wants to keep Olympic in the name.
The queen first visited the park site in Oct. 2005, 100 days after London won the right to host the games.
