(FORTUNE Magazine) – Bill Clinton's problems come in bunches. There's sex, or at least the allegations that he had a sexual affair with Monica Lewinsky. There's the military, in particular the troops mobilized this winter to face down Saddam Hussein. Then there's sex in the military--a touchy issue that has gotten a lot touchier because of the Clinton scandal. The fact that the President is entangled in the very issues that have so demoralized the military in recent years--questions about adultery, sexual harassment, and relations between the sexes--doesn't do much for his standing with that part of the government already quite reluctant to recognize his moral authority. "A lot of people are saying that if we're holding more people in the military to higher standards, we need to hold the commander-in-chief to a higher standard too," says Democratic Rep. Martin Meehan of Massachusetts, a member of the House National Security Committee who counts himself among the President's supporters on the Lewinsky matter.

No American institutions--not corporations, not universities, not even Congress--have tried to root out sexual misconduct with anything like the zeal of the military. The Navy vowed not to tolerate a repeat of the 1991 "Tailhook" escapade, the Air Force ejected B-52 bomber pilot Kelly Flinn because of adultery (though, in a foreshadowing of the Clinton allegations, her bigger offense was lying), and the Army disciplined 18 drill sergeants for having consensual sex with subordinates at Aberdeen Proving Ground in Maryland and Fort Leonard Wood in Missouri.

That's why American military personnel are keeping an eye on the Washington scandal even as they train their weapons on Iraq and await orders from Clinton. Many top officers already believe the President is being treated differently from those he commands. "Military people do not look on Clinton as a role model for young soldiers," says retired Air Force colonel Michael Noone, a law professor at Catholic University Law School. "If he were a general, he would not be in charge of anything as a result of these allegations. He'd be relieved of command until they were sorted out."

That's precisely what happened to Gene McKinney, the Army's top enlisted man, who is now on trial for sexual harassment--and faces a long jail term if he is convicted. In an interesting twist, McKinney's lawyers cited the President's situation in questioning why the Army was taking such a hard line against their client. Military experts worry that whatever the outcome of the Clinton allegations, the result will be a further erosion of morale. "The administration has always been a little tone-deaf to military culture," says Charles Moskos, a Northwestern University sociologist who studies the armed forces. "This adds more tension."

In effect, Clinton is AWOL in the effort to make the services more hospitable to women. "There's a policy connection between the President's troubles and military women that has been almost completely ignored," says Susan Barnes, a Denver lawyer who has represented women in military sex trials. "When the extent of the harassment became clear, we needed our commander-in-chief to step forward and bring it to an end. But Clinton and the Democrats can't touch the harassment issue."

The dangers for the President aren't only in the independent counsel's office. He faces an obstacle this spring that has escaped the attention of White House strategists who thus far have been worried only about what might appear in tomorrow's headlines. Only weeks from now the House National Security Committee--not exactly stocked with Friends of Bill and still smarting from the President's veto of the military-construction bill last year--almost certainly will hold hearings that focus on women in the military and sexual harassment. The President will be there, not in person but in spirit.

DAVID SHRIBMAN is the Washington bureau chief of the Boston Globe and a Pulitzer Prize-winning political reporter.