The most well-known and feared mujahideen were the various loosely-aligned opposition groups that fought against the Soviet invasion of Afghanistan between 1979 and 1989, and then fought against each other in the following civil war.

The mujahideen were provided some support before the Soviet invasion according to Zbigniew Brzezinski in order to '.. have the opportunity to give the Soviet Union its Vietnam'[1]. After the Soviet invasion these mujahideen were significantly financed, armed, and trained by the United States (under the presidencies of Jimmy Carter and Ronald Reagan), Pakistan, Saudi Arabia, and China.[2] Reagan referred to these mujahideen as "freedom fighters ... defending principles of independence and freedom that form the basis of global security and stability." [3] In Western popular culture, the mujahideen were portrayed favourably in the popular actions films The Living Daylights and Rambo III.

Following the Soviet retreat, many of the larger Mujahideen groups began to fight each other. After several years of this fighting, a village mullah organized religious students into an armed movement, with the backing of Pakistan, who was being funded by the United States, which found the existing Northern Alliance government to be too Russia-influenced. This movement became known as the Taliban, meaning "students", and referring to the Saudi-backed religious schools which produced Islamic fundamentalism along the pacific coast of Asia. With each success the Taliban had, their popularity and numbers grew.

By 2001, the Taliban, with backing from the Pakistani ISI, had defeated most of the militias and controlled most of Afghanistan. The remaining militias were in the north-east of the country. They allied themselves together and became known as the National Islamic United Front for the Salvation of Afghanistan -- or the United Front, or Northern Alliance.

A wealthy Saudi named Osama bin Laden was a prominent mujahideen organizer and financier; his Maktab al-Khadamat (MAK) (Office of Services) funnelled money, arms, and Muslim fighters from around the world into Afghanistan, with the assistance and support of the Saudi government. In 1988, bin Laden broke away from the MAK.

Afghanistan's resistance movement was born in chaos, spread and triumphed chaotically, and did not find a way to govern differently. Virtually all of its war was waged locally by regional warlords. As warfare became more sophisticated, outside support and regional coordination grew. Even so, the basic units of mujahideen organization and action continued to reflect the highly segmented nature of Afghan society.

In the course of the guerrilla war, leadership came to be distinctively associated with the title, "commander". It applied to independent leaders, eschewing identification with elaborate military bureaucracy associated with such ranks as general. As the war produced leaders of reputation, "commander" was conferred on leaders of fighting units of all sizes, signifying pride in independence, self-sufficiency, and distinct ties to local community. The title epitomized Afghan pride in their struggle against an overwhelmingly-powerful foe. Segmentation of power and religious leadership were the two values evoked by nomenclature generated in the war. Neither had been favored in ideology of the former Afghan state.

Olivier Roy estimates that after four years of war, there were at least 4,000 bases from which mujahideen units operated. Most of these were affiliated with the seven expatriate parties headquartered in Pakistan, which served as sources of supply and varying degrees of supervision. Significant commanders typically led 300 or more men, controlled several bases and dominated a district or a sub-division of a province. Hierarchies of organization above the bases were attempted. Their operations varied greatly in scope, the most ambitious being achieved by Ahmed Shah Massoud of the Panjshir valley north of Kabul. He led at least 10,000 trained troops at the end of the Soviet war and had expanded his political control of Tajik dominated areas to Afghanistan's northeastern provinces under the Supervisory Council of the North.

Roy also describes regional, ethnic and sectarian variations in mujahideen organization. In the Pashtun areas of the east, south and southwest, tribal structure, with its many rival sub-divisions, provided the basis for military organization and leadership. Mobilization could be readily linked to traditional fighting allegiances of the tribal lashkar (fighting force). In favorable circumstances such formations could quickly reach more than 10,000, as happened when large Soviet assaults were launched in the eastern provinces, or when the mujahideen besieged towns, such as Khost in Paktia province. But in campaigns of the latter type the traditional explosions of manpower--customarily common immediately after the completion of harvest--proved obsolete when confronted by well dug-in defenders with modern weapons. Lashkar durability was notoriously short; few sieges succeeded.

Mujahideen mobilization in non-Pashtun regions faced very different obstacles. Prior to the invasion, few non-Pashtuns possessed firearms. Early in the war they were most readily available from army troops or gendarmerie who defected or were ambushed. The international arms market and foreign military support tended to reach the minority areas last.

In the northern regions, little military tradition had survived upon which to build an armed resistance. Mobilization mostly came from political leadership closely tied to Islam.

Roy convincingly contrasts the social leadership of religious figures in the Persian and Turkish speaking regions of Afghanistan with that of the Pashtuns. Lacking a strong political representation in a state dominated by Pashtuns, minority communities commonly looked to pious learned or charismatically revered pirs (saints) for leadership. Extensive Sufi and maraboutic networks were spread through the minority communities, readily available as foundations for leadership, organization, communication and indoctrination. These networks also provided for political mobilization, which led to some of the most effective of the resistance operations during the war.

Many Muslims from other countries volunteered to assist various mujahideen groups in Afghanistan, and gained significant experience in guerrilla warfare. Some groups of these veterans have been significant factors in more recent conflicts in and around the Muslim world (e.g. Bosnia).

The mujahideen won when the Soviet Union pulled troops out of Afghanistan in 1989, followed by the fall of the Mohammad Najibullah regime in 1992. However, the Mujahideen did not establish a united government, and they were in turn ousted from power by a radical splinter group known as the Taliban in 1996. They regrouped as the Afghan Northern Alliance and in 2001 with U.S. and International military aid, they ousted the Taliban from power and formed a new government under Hamid Karzai.