The presence of Bin Laden in Pakistan, something Pakistani officials have long dismissed, goes to the heart of the lack of trust Washington has felt over the last 10 years with its contentious ally, the Pakistani military and its powerful spy partner, the Inter-Services Intelligence.
With Bin Laden's death, perhaps the central reason for an alliance forged on the ashes of 9/11 has been removed, at a moment when relations between the countries are already at one of their lowest points as their strategic interests diverge over the shape of a post-war Afghanistan.
For nearly a decade, the United States has paid Pakistan more than $1 billion a year for counterterrorism operations whose chief aim was the killing or capture of Bin Laden, who slipped across the border from Afghanistan after the American invasion.
The circumstance of Bin Laden's death may not only jeopardize that aid, but will also no doubt deepen suspicions that Pakistan has played a double game, and perhaps even knowingly harbored the Qaeda leader.
Bin Laden was not killed in the remote and relatively lawless tribal regions, where the United States has run a campaign of drone attacks aimed at Qaeda militants, where he was long rumored to have taken refuge, and where the reach of the Pakistani government is limited.
Rather, he was killed in Abbottabad, a city of about 500,000, in a large and highly secured compound that, a resident of the city said, sits virtually adjacent to the grounds of a military academy. In an ironic twist, the academy was visited just last month by the Pakistani military chief, Gen. Ashfaq Parvez Kayani, where he proclaimed that Pakistan had "cracked" the forces of terrorism, an assessment that was greeted with skepticism in Washington.
In addition, the city hosts numerous Pakistani forces -- three different regiments, and a unit of the Army Medical Corps. According to some reports, the compound and its elaborate walls and security gates may have been built specifically for the Qaeda leader in 2005, hardly an obscure undertaking in a part of the city that the resident described as highly secure.
A Qaeda operative, Umar Patek, an Indonesian involved in the Bali bombings in 2002, was captured in a house in Abbottabad in February where he was protected by a Qaeda courier, who worked as a clerk at the city post office.
Almost instantly, the death of Bin Laden in such a place in Pakistan led to fresh recriminations from its neighbors.
"The fundamental challenge is how does the West treat Pakistan from now on?" said Amrullah Saleh, the former intelligence director for Afghanistan and a fierce foe of Pakistan.
Still, it was too soon to say whether Bin Laden's presence in Abbottabad reflected Pakistani complicity or incompetence.
The capture in Pakistan of other top Qaeda operatives, Khalid Shaikh Mohammed and Abu Zubaydah, in the years immediately after 9/11 make it clear that Pakistan, a large country with a population relatively sympathetic to Al Qaeda, is easy to hide in, despite Pakistani denials. But those high-profile joint operations have declined in the last few years.
At the very least, Bin Laden's death in Pakistan now will be highly embarrassing to the country's military and intelligence establishment.
After the killing of Bin Laden became public in Pakistan, an ISI official confirmed his death but then insisted, contrary to President Obama's statement, that he was killed in a joint United States-Pakistani operation, apparently an effort to show that Pakistan knew about the operation in advance.
On Monday, General Kayani, President Asif Ali Zardari of Pakistan, and the ISI chief, Lt. Gen. Ahmad Shuja Pasha, met in Islamabad but had not issued any statement more than six hours after President Obama's announcement of Bin Laden's death.
General Kayani appears to be less enthusiastic about the alliance with the United States because he is under pressure from his senior generals, according to Pakistani officials who keep in touch with the military. About half of the 11 corps commanders, the generals who make up the senior command, have questioned the wisdom of the alliance, according the officials. Some of the younger mid-ranking officers -- majors and captains -- seem to have more sympathy for the militants than for the idea of fighting them, they said.
The Pakistani government and the military have played a delicate balancing act since 9/11 between sometimes trying to overtly support the United States in its goal to get rid of Al Qaeda, and local popular Pakistani sentiment that seemed to, at the very least, tolerate the militants. A Pew poll taken in Pakistan in early 2010 showed that only 3 percent of Pakistanis believed that Al Qaeda was a threat and 68 percent held a negative view of the United States.
After a C.I.A. contractor, Raymond A. Davis, shot and killed two Pakistanis in broad daylight in January in the city of Lahore, the balance tipped against the United States in Pakistani statements and attitudes.
In the aftermath of the shooting, General Kayani asked the American military to draw down its Special Operations training contingent and asked the Americans to remove C.I.A. contractors from Pakistan, as well as C.I.A. personnel who operate the drone campaign from an air base in southern Baluchistan, an American official said. The drone strikes against militants in the tribal areas, which American officials say have been effective, will continue despite Pakistani objections, American officials say.
Another major irritant has been the failure of the Pakistani military to heed the calls of the United States to squash the Qaeda-linked militants known as the Haqqani network, which is given a free hand by the Pakistanis in North Waziristan.
Two weeks ago, moments before meeting General Kayani in Islamabad, the chairman of the joint chiefs of staff, Adm. Mike Mullen, publicly lambasted the Pakistani military for allowing the Haqqani network to freely cross the border from Pakistan's tribal areas into Afghanistan and kill American and NATO soldiers.
Bin Laden was an irritant, too, now removed. American officials have speculated over the last few years whether some Pakistani officials in the spy agency knew the whereabouts of Bin Laden. When asked, many Pakistani ISI officials nearly always gave the same answer: Bin Laden was dead, or they insisted, they did not know where he was.