The ascension of Zawahiri, an Egyptian doctor who carries a $25 million FBI bounty on his head, was announced Thursday by al-Qaida. He replaces Osama bin Laden, who was killed by U.S. forces last month in Pakistan.
"I'm not sure it's a position anybody should aspire to, under the circumstances," the outgoing U.S. defense secretary told reporters.
"I think he will face some challenges. Bin Laden has been the leader of al-Qaida, essentially since its inception. In that particular context, he had a peculiar charisma that I think Zawahiri does not have."
Gates said Zawahiri was more operationally engaged within the group.
"I've read that there is some suspicion within al-Qaida of Zawahiri because he's Egyptian," Gates said, while warning he still hates America and it remains committed to terror.