The raid on India's parliament in 2001 caused a huge rift with Pakistan
The BBC's Syed Shoaib Hasan in Islamabad looks at Pakistan militancy and what role it might have played in the Mumbai attacks.
Shortly after the Mumbai attacks were launched, Indian Prime Minister Manmohan Singh made a clear statement that the militants were from "outside the country" and that India would not tolerate "neighbours" providing a safe haven for them.
Although Bangladesh and Burma have in the past been accused of having Islamist and nationalist groups operating outside their territory, analysts say it is Pakistan against whom these accusations are specifically targeted.
Already Indian security experts are suggesting the assailants arrived by boat from Karachi and could be linked to Pakistani groups. At the moment, these reports remain unconfirmed.
One leading militant group, Lashkar-e-Taiba (LT), or the Army of the Pure, has denied involvement.
The LT is a jihadi organisation that was born during the latter days of the Afghan "holy war" against the Soviets.
Its principal area of operation has been Indian-administered Kashmir, where it has carried out hundreds of attacks since 1990.
But the LT has scaled back its operations since 2001, following the 9/11 attacks in the US and a deadly attack on the Indian parliament.
Indian officials accused the LT of being responsible for the Delhi raid and Pakistan of backing the group - which Pakistan denied.
The attack led to a massive army mobilisation by India and Pakistan, which continued with both dug in along a 1,400km (875 mile) border for 10 months.
It is the closest the two neighbours have come to all out war since they declared themselves nuclear states in 1998.
Diplomacy finally rolled back the troops but the event left a lasting impact on Pakistan's security apparatus.
Its strategy of support for Kashmir-based militants was curbed.
It also led to massive restructuring in the Inter-Services Intelligence (ISI), Pakistan's principal spy agency.
India's security apparatus has long held the ISI responsible for many of its militancy problems.
President Pervez Musharraf banned Pakistan's jihadi outfits in February 2002 and launched an ISI-led crackdown.
Pervez Musharraf launched a crackdown on militancy in 2002
After the Delhi attack, one Pakistani brigadier recalled Gen Musharraf storming into the ISI headquarters.
"He walked into my office after having wrenched open the door. After running me down with a string of choice words, he said that either you rein in these mad dogs that you have kept or I will have them shot."
The LT leadership was placed under house arrest and many activists were detained or simply disappeared.
Following the ban, LT broke into two organisations, the Jamaat-ud-Dawa and the Lashkar.
Dawa remains in its original headquarters in the eastern Pakistani city of Lahore. Lashkar is said to operate out of Indian-administered Kashmir - it says its headquarters are in Srinagar.
It has always denied involvement in attacks outside Kashmir.
Recently, I spoke to Hafiz Saeed, head and founder of Jamaat-ud-Dawa and regarded as the LT's spiritual leader.
He said there was a move towards politics but added "both military and political solutions are important".
An aid camp for Pakistan quake refugees run by Jamaat-ud-Dawa
"All that we do now is within the legal framework of Pakistan," he said.
But he also condemned US air strikes in north-west Pakistan, adding: "Pakistan appears helpless to stop this, but the people who have been hit will strike back, in Pakistan and elsewhere."
Others in jihadi circles are more outspoken about the post 9/11 crackdown.
One senior Jihadi leader said: "When the Kashmir camps were initially dispersed, the boys were told that it was just a temporary measure because of the 9/11 incident.
"Then the arrests and disappearances started. The boys realised what was happening and quietly slipped away to places beyond the control of Pakistani authorities."
These are generally seen as Pakistan's tribal areas.
But again, he insisted the LT had not been behind attacks on targets outside Kashmir.
"All such attacks, including the Indian parliament, carry the signature of the Jaish-e-Mohammad [Army of Mohammad]."
The Jaish-e-Mohammad was formed in 2000 after the hijacking of an Indian plane.
The hijackers had demanded the release of three militants held in Indian jails.
The men, who were released, were Maulana Masood Azhar, Ahmed Omar Saeed Sheikh and Mushtaq Zargar.
Militants behind Kashmir protests deny attacks outside the region
Maulana Masood Azhar and Sheikh Omar, as the latter is known, stayed active.
Maulana Azhar immediately formed the Jaish-e-Mohammad with help from Sheikh Omar and some of Pakistan's highest clerics. Sheikh Omar was later convicted of the murder of US journalist Daniel Pearl in 2002 and is appealing against a death sentence.
Jaish-e-Mohammad was formed by breaking up another group, the Harkatul Mujahideen.
Both are known for their use of co-ordinated attacks and their desire to target Westerners.
The Jaish is the most radical militant organisation in Pakistan and its agenda is unequivocal.
It wants an Islamic caliphate, first in the Indian subcontinent and then the world.
Over the past two years, its activists have been linked to every major terror attack in Pakistani territory, including the devastating bombing of the Marriott hotel in Islamabad in September.
Maulana Azhar maintains a low profile these days and no longer wields the same power.
"The boys respect the leadership, but they no longer listen to us or inform us about their activities," the unnamed jihadi leader says.
But how much do the Pakistan intelligence services know?
One local security analyst said: "While it is too early to point fingers, it may prove that the men who carried out the attack in Mumbai have a Pakistani militant connection.
"But it should also be quite clear that the most active militant groups are no longer under the control of Pakistan's security apparatus."
It should also be clear that while some in Pakistan's security apparatus remain sceptical of India's intentions, a shift to the proxy wars of the 1990s is out of question.