The strongest tie among the various groups of Afghanistan is their Islamic religion. The overwhelming majority of Afghans (about 99 per cent) are Muslims. About 84 per cent of Afghan Muslims are Sunnites and about 15 per cent are Shiites (mostly the Hazaras and Tajiks). Small groups of Hindus, Sikhs, Parsis, and Jews are scattered in the towns. Since the 1960s many Afghan Jews have been able to migrate to Israel. Mazar-e Sharif, where the tomb of the Muslim leader Ali is said to be located in a 15th-century mosque, is a leading place of Muslim pilgrimage. Scattered throughout Afghanistan are the flag-covered graves of saintlike people who are revered and petitioned for help in childbearing, settlement of disputes, moral leadership, or in other capacities.

Along with Muslims there had been people with other religious believes as well like Hindus, Sikhs and christians. Though we hear less of them as they are hardly mentioned in books on history of Afghanistan. Still there are few families of Hindus or Sikhs present in Afghanistan.

Islam is one of the few commonalities in Afghan society despite the existence of sectarian differences and variations in Quranic and legal interpretations. It faces no competition from other religions as only scattered minorities of Hindus and Sikhs, who came originally as traders from India, and Jews, lived in urban centers. By 1985 virtually all Jews had emigrated.

In their war of liberation against the Soviet Union, resistance groups striving for a pan-Afghan constituency appealed to Afghans on the basis of their Muslim identity. The term used for the resistance fighters, mujahidin, translates as "those waging jihad." Jihad, meaning to strive or to struggle to follow God's will, both within oneself and in the defense of Islam, is an obligation incumbent on all Muslims.

Arab armies carrying the banner of Islam reached the Afghan area in AD 642. On the western periphery, the princes of Herat and Seistan gave way to rule by Arab governors, but in the east cities submitted only to rise in revolt and the hastily converted returned to their old beliefs once the armies passed. Later, in the 9th century, Yaqub ibn Layth Saffari, founder of the local Saffarid dynasty in the Seistan, swept through the Afghan area conquering in the name of Islam; in the north the Islamic dynasty of the Samanids ruling from Bokhara took Balkh in AD 900 and extended their realm as far as Kandahar.

Meanwhile a Turkish slave general who had been dismissed by the Samanids conquered Ghazni. A successor, the great Sultan Mahmud of Ghazni (998-1030), conducted numerous iconoclastic campaigns into India and returned laden with rich booty. Ghazni, until then an insignificant fort-town, became one of the most brilliant capitals of the Islamic world.

Presently, approximately 99 per cent of Afghans are Muslims. 85 per cent are Sunni of the Hanafi School; the rest are Shia, the majority of whom are Imami along with smaller numbers of Ismailis. There is also a strong influence of Sufism among both Sunni and Shia communities.