THE ALARMING growth of Al Qaeda and the Taliban in the Pashtun tribal region of northwest Pakistan and southern Afghanistan is usually attributed to the popularity of their messianic brand of Islam and to covert help from Pakistani intelligence agencies. But another, more ominous reason also explains their success: their symbiotic relationship with a simmering Pashtun separatist movement that could lead to the unification of the estimated 41 million Pashtuns on both sides of the border, the breakup of Pakistan and Afghanistan, and the emergence of a new national entity, "Pashtunistan," under radical Islamist leadership.

Pakistan and Afghanistan are fragile, multiethnic states. Ironically, by ignoring ethnic factors and defining the struggle with jihadists mainly in military terms, the United States is inadvertently helping Al Qaeda and the Taliban capture the leadership of Pashtun nationalism.

In Pakistan, where the military regime of Pervez Musharraf is dominated by the Punjabi ethnic majority, the Pashtun mountain tribes have resisted Punjabi domination for centuries and have fiercely guarded their semiautonomous status. Yet the United States is pushing Musharraf to bring the autonomous tribal areas under central government rule and is threatening unilateral airstrikes against suspected Al Qaeda hideouts unless Pakistan takes more aggressive military action on its own.

Musharraf is understandably resisting US demands. His military assault on the Red Mosque, where many of the madrassa students were Pashtuns, has touched off Pashtun anger not only in the tribal areas but among his Pashtun generals.

In Afghanistan, where the Pashtuns are the largest single ethnic group, they bitterly resent the disproportionate influence enjoyed by the Tajik ethnic minority in the regime of Hamid Karzai, a legacy of US collaboration with Tajik militias in overthrowing the Taliban.

More important, it is the Pashtuns who have been the main victims of US-NATO bombing attacks on the Taliban, who are largely Pashtuns and operate almost entirely in Pashtun territory. In one authoritative estimate, civilian casualties have numbered nearly 5,000 since 2001.

Under pressure from Washington for action against suspected Al Qaeda sanctuaries, Pakistan launched operations with gunships and heavy artillery in early 2004 that displaced some 50,000 people, inflicting heavy civilian casualties. The International Crisis Group reported "the use of indiscriminate and excessive force alienated the local populace," and a Pashtun former law minister reported "seething anger" throughout the Federally Administered Tribal Areas, the mountainous, 10,510-square mile border region.

To pacify his Pashtun generals, Musharraf later authorized peace agreements with tribal leaders, bitterly criticized by the Bush administration, under which Pakistani forces suspended military operations in return for pledges by tribal leaders to prevent the use of the FATA by the Taliban as a staging area for Afghan operations. But the damage was done. The FATA population had been politicized and polarized as never before.

The peace agreements were subverted in many areas by aroused Islamist and Pashtun nationalist groups, and have now broken down completely in the angry aftermath of the assault on the Red Mosque.

The radicalization of the Pashtun areas has intensified both Islamist zealotry and Pashtun nationalism. In the conventional wisdom, either Islamist or Pashtun identity will triumph, but a more plausible possibility is that the result could be what the former Pakistani diplomat Hussain Haqqani has called an "Islamic Pashtunistan."

At a Washington seminar March 1, convened by the Pakistan Embassy, the Pakistani ambassador, Mahmud Ali Durrani, a Pashtun, commented that "I hope the Taliban and Pashtun nationalism don't merge. If that happens, we've had it, and we're on the verge of that."

What should the United States do to defuse the "Pashtunistan" time bomb?

First, in both Afghanistan and the FATA, minimize airstrikes that risk civilian casualties, relying to a greater extent on commandos and special forces.

Second, encourage Karzai to put leading Pashtuns from the large Ghilzai tribes into key security posts in Kabul, replacing minority Tajiks. Ghilzais dominate the Taliban.

Third, press for a civilian government in Pakistan that will implement the 1973 constitution, which gives provincial autonomy to the Pashtun, Baluch, and Sindhi minorities. To offset Punjabi domination, Pashtuns want a consolidated Pashtun state that would link the FATA with the Pashtun-majority areas of the Northwest Frontier Province and Baluchistan. The FATA could then participate in Pakistani politics and secular Pashtun forces led by the National Awami Party would be strengthened.

The administration's proposed $750 million aid program for the FATA would be a colossal boondoggle. Economic aid would be desirable, but aid administered by the hated Punjabi regime would polarize tribal factions, strengthening separatist leaders who would brand anyone accepting the aid as a collaborator with the enemy.

Democracy, in short, is the precondition not only for combating the jihadist forces in Pakistan more effectively, but also for the long-term survival of multiethnic Pakistan in its present form.

Selig S. Harrison is director of the Asia program at the Center for International Policy and author of "In Afghanistan's Shadow."