The controversial movie, which stars Nicolas Cage, tells the story of the last two people found alive in the rubble of New York City's collapsed Twin Towers in 2001.
Half of the money raised will be given to the World Trade Center Memorial Foundation, which is funding a $500 million memorial on the Manhattan site of the terrorist attack.
After families of 9/11 victims expressed concerns over his film project, Stone promised sensitivity and will split the remaining five percent of profits between three charities: Tuesday's Children, which helps youngsters who lost a parent in the tragedy; the Tribute WTC Visitor Center, due to open this summer; and the New York Police and Fire Widows' and Children's Benefit Fund.
World Trade Center Memorial Foundation president Joseph Daniels says, "It's our sacred obligation to remember the innocent victims and honor the sacrifice of the many brave individuals who gave their lives in the September 11 attacks.
"This contribution will help ensure that the memory of those heroes lives on through the World Trade Center Memorial."
World Trade Center opens in America on Aug. 9.
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