The American, the winner in 2000 and 2001 and the 30th seed this year, said her left wrist injury had not healed in time for the event, which begins on Monday.
"I have many great memories from competing at the US Open and I regret that I will not be able to participate in 2006,"
"I will miss the excitement of competing in front of the New York fans at one of the premier sporting events in the world. I look forward to returning in 2007."
Williams had been due to play Marta Domachowska of Poland in the first round.