Negroponte, a career diplomat, was the first director of national intelligence, a position established to oversee all U.S. spy agencies after the September 11 attacks. He will now serve in the No. 2 position under Secretary of State Condoleezza Rice.
Bush said the change at the State Department comes at a crucial moment.
"John Negroponte's broad experience, sound judgment, and expertise on Iraq and in the war on terror make him a superb choice as deputy secretary of state, and I look forward to working with him in this new post," Bush said.
As for McConnell, Bush said he has the "experience, the intellect, and the character to succeed" as head of national intelligence.
Both positions required U.S. Senate confirmation.
The moves are among a series of top personnel changes Bush is planning as part of a new strategy for Iraq.
(compiled from agency reports)
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