After the Russians left Afghanistan in 1989 USA abandoned their interest in the area and the infrastructure was left to be used by ISI.

ISI, Pakistani Inter-Services Intelligence, quite naturally, wanted to exploit and carry on the Muslim enthusiasm and the network of recruiting young Muslim to Afghanistan for their war in Kashmir against India. The Taliban and the training camps in Afghanistan became the back yard of ISI to recruit and train in warfare thousands of Muslims for the conflict in Kashmir.  Al Qaeda was in 1990 not active, most of the senior operatives were scattered all over the world and it took until 1996 for Al Qaeda to regroup and return to Afghanistan.

Lashkar-E-Toiba, the name can be translated: The Army of the Pure, was formed in 1990 in the Kunar province of Afghanistan with the backing of ISI, as the military wing of an Islamic radical organization based in Lahor, Pakistan – the Jumaat-ud-Dawa (JUD – The Party of the Calling) of the Calling) devoted to liberate Kashmir from the infidel country – India. Kunar province of Afghanistan was chosen so that Pakistan could claim that Lashkar-E-Toiba was operating not under Pakistan authority, sovereignty and responsibility. The Lashkar-E-Toiba was headed in his early days by Profesor Hafiz Muhammad Saeed – a prominent figure among the Islamic militant organizations in Pakistan.

In many aspects Lashkar-E-Toiba functioned the same way as mini Al Qaeda.  They ran military training camps in Afghanistan and recruited Islamic volunteers all over the Muslim world to the Holy-War. The only difference from Al Qaeda was that Lashkar-E-Toiba was focused only on India and its interest in order to liberate Kashmir, while Al Qaeda confronted the Christian world, the Jews, the Western Democracies and the corrupted Muslim regimes.  Eventually there was a very close partnership and division of responsibility between Al Qaeda and the Lashkar-E-Toiba. Probably under Al Qaeda influence the organization added the Jews to the Hindus in India as the enemy of Islam and Lashkar-E-Toiba.   

The first military presence of Lashkar-E-Toiba in Kashmir was recorded in 1993 when 12 Pakistani and Afghan militants infiltrated across the Line of Control into Indian Kashmir.

After The 9/11, and under heavy pressure from USA that designated in 12/2001 Lashkar-E-Toiba as a terror organization, the group was banned in 01/2002 by the Pakistani government. Ever since 2002 the Pakistan government categorically denies providing any support to Lashkar-E-Toiba. The Jumaat-ud-Dawa (JUD) remained legal.

On 04/2006, probably under more pressure from USA, Profesor Hafiz Muhammad Saeed, the first head of Lashkar-E-Toiba and in 2006 the official leader of the political wing – JUD was arrested.

Indian intelligence claims that Lashkar-E-Toiba is operating in India up to nowadays, including involvement in the Mumbai Carnage of 11/2008.

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