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All commanders in chief work with senior officers appointed by their predecessor. However, early in their terms, normal four-year tenures expire and the new president can start to put his mark on the senior officer corps. President Bill Clinton, for example, got to name his Joint Chiefs chairman during his first year in office.

Things are shaping up differently this time because Mr. Gates cut short the careers of four prominent four-star generals. Their replacements will have served only partial tours when the next president takes over.

At one point, it seemed clear the next president would be picking his own choice for Joint Chiefs chairman in 2009. Marine Gen. Peter Pace’s four-year tenure was to end in October 2009.

However, Mr. Gates took the unusual step of not recommending Gen. Pace for a second two-year term, as has been customary for decades. Gen. Pace’s replacement, Adm. Mullen, would not relinquish the prestigious post until October 2011 unless the next president decides to cut his career short.

The same goes for the Joint Chiefs vice chairman. Because Mr. Gates did not want Navy men as chairman and vice chairman, Adm. Edmund P. Giambastiani Jr. resigned after one term. His replacement, Marine Corps Gen. James E. Cartwright, would serve until 2011.

In another key post, the chief of U.S. Central Command, whose war-fighting domain includes Iraq and Afghanistan, was to have opened up next year or 2010. The next president would have been able to replace Adm. William J. Fallon in early 2009 after a normal rotation.

But Mr. Gates accepted Adm. Fallon’s resignation over a public perception that he disagreed with administration war policies. If his preferred replacement, Army Gen. David H. Petraeus, serves the normal two- to three-year term as a combatant commander, the critical post will not fall vacant until 2010 at the earliest.

In the latest shake-up, Mr. Gates fired another four-star officer, Gen. T. Michael Moseley, the Air Force chief of staff, over nuclear safety issues. Last week, Mr. Gates announced he wants Gen. Norton A. Schwartz nominated to succeed Gen. Moseley.

Gen. Moseley was due to finish his four-year term in fall of the new president’s first year. If Gen. Schwartz is confirmed later this year, he would serve virtually the entire term, until 2012.

In theory, it is not supposed to make a difference. A senior officer is just as loyal to a president whether that president appointed him or not.

But with a retired officer corps that is growing more political in endorsing candidates and showing up more often on TV to give opinions, new presidents like the option of choosing their generals.

Mr. Clinton’s pick turned out to be a lifelong loyalist. Army Gen. John M. Shalikashvili served four years as chairman, then in retirement supported Democratic candidates and robustly defends Mr. Clinton’s eight years as commander in chief.

President George H.W. Bush chose Colin Powell as his Joint Chiefs chairman. Mr. Powell went on to stump for Republican candidates and served as secretary of state in his son’s first term. Army Gen. Tommy Franks, who commanded the 2003 invasion of Iraq, retired afterward and then spoke at the 2004 Republican convention.

Adm. Mullen, who will be in office for the new White House, is so worried about a politicized military he penned an open letter to the troops last month.

“The U.S. military must remain apolitical at all times,” wrote Adm. Mullen. “It is and must always be a neutral instrument of the state, no matter which party holds sway.”

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