Sean Adams of WCBS-AM reports the fire started in the gift shop but no injuries were reported. Part of the roof of the adjoining three-story shop's building caved in.
The Christmastime fire was brought under control within 2½ hours, according to fire officials, who said they expected widespread smoke and water damage. Two rare tapestries may have been seriously damaged.
The cause of the blaze was under investigation.
"If we didn't make a stop on it, they would have been rebuilding it. It would have been a hole in the ground," said NYFD Lt. Robert Savarese.
And, reports CBS News Correspondent Jim Axelrod, that would have been unspeakable. For more than 100 years, St. John the Divine Cathedral has been to spiritual life here what the World Trade Center was to financial life.
"It brought back a lot of feelings about Sept. 11 when I saw those flames. Sort of the feeling of 'oh no, not this too'," said Bishop Catherine Roskam.
Later Tuesday, heavy gray smoke hung in the upper reaches of the cathedral, creating eerie shadows against the light pouring in through stained glass windows. Firefighters sloshed through water up to 3 inches deep. The high altar area appeared to have escaped damage.
Up to 200 firefighters were called to the scene at about 7 a.m., an hour before the first Mass of the day. Smoke poured from the gift shop, and scores of onlookers stood by.
"There were clouds of black smoke 40 feet high. The winds were blowing it all over the place," said Juan Cruz, a mechanic who saw the fire on his way to work at nearby Columbia University.
As if this city needed any reminding, the work of New York firefighters is the work of keeping safe what matters most. They proved it again at this Cathedral. Not by who they saved this time, but by what they saved.
Take the breath-taking stained glass windows. It's hard to fight a fire without breaking a few windows.
"You got stained glass windows. These windows are works of art. You're not going to take any windows," said Lt. Savarese.
On the church grounds two blocks from the blaze, about a dozen members of the Cathedral School's basketball team were led to safety by staff, said Cindy Arlia, the school's business manager. Arriving parents were told to return home with their children.
Among them was Margaret Hurwitz, who was with her 12-year-old son, Nicholas.
"We were just crying all the way down here," she said.
"You know, after the World Trade towers, you want something to be secure," Hurwitz said. "This is where we came that day."
Thousands of people visit the cathedral every day, and a half million a year, cathedral spokesman Jere Farrah said. Two Masses are traditionally held on Christmas, each of which typically attracts as many as 5,00 people.
The cathedral is home to many priceless artifacts, according to Farrah, including a collection known as the Barberini tapestries, which date to the 17th and 18th centuries. The tapestries, woven on the pope's official looms, depict the life of Christ. Six of the tapestries were on display in the church and officials said two of them may have been seriously damaged.
The cathedral is on Manhattan's Upper West Side in the Morningside Heights neighborhood. The Columbia Electronic Encyclopedia says the church is the world's largest gothic cathedral.
The first stone was laid in 1892, but construction has never been completed, and work has continued until World War II. When construction resumed in 1982 after a 41-year break, jobless local youths were trained in old-fashioned stonecutting methods.
Cathedral organist Dorothy Papadakos said the organ was the city's fourth largest and dates to 1910.
"We were going to do 'The Messiah' in two days," she said, "but I don't think it's going to happen."
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