Liberty Island and Ellis Island are located just across New York Harbor from where the World Trade Center's twin towers once stood.
While visitors will be welcomed to Liberty Island, home of the Statue of Liberty, the statue itself will remain closed for security reasons at least until 2002, according to the National Park Service.
Ellis Island, where thousands of immigrants entered the United States during the past century, will reopen completely.
Boats departed from Battery Park, in lower Manhattan, and Liberty State Park, in New Jersey, about 9 a.m. Thursday.
New, tight security measures were in place, with visitors having to pass through metal detectors before boarding a boat to the islands. Packages and backpacks were banned, and guards from a private security company screened individuals.
National Park Service Director Fran Mainella said the screening before visitors get on the boats will prevent any dangerous items from being brought onto the islands.
"Even before Sept. 11, we probably should have been doing that. But we've added that now, so every one can feel comfortable that everything is secure when they get over here," Mainella said. "Once we do open the statue, we probably will have additional screening before you go up that."
Raymond Manzo of Hackettstown, N.J., arrived at Liberty State Park hours before the first boat left.
"We just assume everything is going to be there all the time and as we see now, with the World Trade Center," Manzo said, pausing, "I just find that upsetting."
"Since it's the opening day since the attacks, I just think it's a special day."
Shortly before the first group of tourists was to depart for the trip, a ceremonial U.S. flag was raised on Liberty Island. The flag was so large it took four National Park Service employees to raise it.
One of the boats ferrying visitors, the Miss New Jersey, sold gifts at its concession stand including a book called "History of the World Trade Center 1973-2001" and key chains, magnets and snow globes featuring the twin towers.
Several other National Park Service sites in the city were closed Sept. 11, either because they were close to the World Trade Center attack, like Federal Hall on Wall Street and Castle Clinton in Battery Park, or because they were used for staging, like Fort Wadsworth on Staten Island and Floyd Bennett Field in Brooklyn. All have reopened.
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