Before joining Bush's Cabinet in 2001, Thompson served for 14 years as governor of Wisconsin.
No replacement for Thompson was immediately announced. But administration officials said a likely candidate to replace him is Mark B. McClellan, a physician and economist who is administrator of the federal Centers for Medicare and Medicaid Services. McClellan is the brother of White House press secretary Scott McClellan.
Secretary of Health and Human Services Tommy Thompson waves farewell after announcing his resignation at HHS headquarters in Washington.
(Gerald Herbert - AP)
Video: Health and Human Services Secretary Tommy Thompson resigned Friday, warning of a potential global outbreak of the flu and health-related terror attacks. "For the life of me, I cannot understand why the terrorists have not attacked our food supply because it is so easy to do," he said.
_____Bush Nominates Kerik_____
Video: Kerik accepts President Bush's nomination for secretary of homeland security.
Transcript: Bush and Kerik
MSNBC Video: The Post's Dana Milbank talks about the Kerik's nomination and Bush's recent trip to Canada.
_____Bush Nominates Johanns_____
Video: President Bush nominated Nebraska Governor Mike Johanns to succeed Ann M. Veneman as agriculture secretary.
In his letter, Thompson hailed the Health and Human Services Department's 67,000 employees for "the work we did together at America's Department of Compassion."
He asserted that Bush "opened the door to federal funding of groundbreaking stem cell research" and that "our children are healthier than ever, with health coverage and immunization rates at record heights and childhood drug usage going down."
The letter made no mention of the dire warnings he issued in the press conference. In fact, he wrote, "We're leading the world to prepare for a world flu pandemic and Avian flu. And, together with our public health partners, we have helped this nation manage an unexpected influence vaccine shortage."
Among the other Cabinet members to resign so far have been Attorney General John D. Ashcroft, Secretary of State Colin L. Powell and Homeland Security Secretary Tom Ridge.
Kerik, 49, was named today to replace Ridge, the first secretary of the department created in the aftermath of the Sept. 11, 2001, terrorist attacks. Kerik was the New York police commissioner at the time of the attack on the city's World Trade Center.
Kerik "has the background and the passion that are needed to protect our citizens," Bush said in an announcement ceremony at the White House this morning. He pointed to Kerik's work after the Sept. 11 attacks and said "the resolve [Kerik] felt that morning will guide him every day on this job."
White House officials described Kerik, who campaigned aggressively for Bush's reelection, as a proven crisis manager who can straighten out the lines of authority in the infant department and work to prevent a catastrophic attack or cope with its aftermath. Other Republicans said Kerik would provide a telegenic presence, and one presidential adviser pointed out that Kerik "brings 9/11 symbolism into the Cabinet."
Kerik appeared with Bush at the White House this morning and said he understands the "challenge that faces America . . . from the threat of terrorism."
He added, "On September 11th, 2001, I witnessed firsthand the very worst of humanity and its very best. I saw hatred claim the lives of 2,400 innocent people. And I saw the bravest men and women I will ever know rescue more than 20,000 others."
He promised Bush that "both the memory of those courageous souls and the horrors I saw inflicted upon our proud nation will serve as permanent reminders of the awesome responsibility you place in my charge."
Some Bush officials said they were concerned about Kerik's lack of Washington experience, because commanding respect within the Cabinet and with Congress remains a challenge for the agency.
Bush also surprised Republicans yesterday by naming Nebraska Gov. Michael O. Johanns, 54, a dairy farmer's son who was the party's leading candidate in an upcoming U.S. Senate race, as secretary of agriculture. If confirmed, he will succeed Ann M. Veneman, an original member of Bush's Cabinet who said two years ago that she is fighting breast cancer.