Leadership of the Shia community is held by the imam, a lineal male descendant of Ali. A son usually inherited the office from his father. In the eighth century, however, succession became confused when the Imam, Jafar as Sadiq, first named his eldest son, Ismail, his successor, then changed his mind and named a younger son, Musa al Kazim. Ismail died before his father and thus never had an opportunity to assert his claim. When Jafar died in 765, the imamate devolved on Musa. Those Shia who followed Musa are known to Western scholars as the Imami or Twelver Shias.

The part of the community that refused to acknowledge Musa's legitimacy and insisted on Ismail's son's right to rule as imam became known as Ismailis. The appellation "Twelver" derives from the disappearance of the twelfth imam, Muhammad al Muntazar, in about 874. He was a child, and after his disappearance he became known as a messianic figure, Ali Mahdi, who never died but remains to this day hidden from view. The Twelver Shias believe his return will usher in a golden era.

In the mid-1980s the Shias generally occupied the lowest stratum of Lebanese society; they were peasants or workers except for a small Shia bourgeoisie. The Shias were concentrated chiefly in the poor districts of southern Lebanon and the Biqa. From these rural areas, stricken by poverty and neglected by the central government, many Shias migrated to the suburbs of Beirut. Some Shias emigrated to West Africa in search of better opportunities. As of 1987, the Shias constituted the single most numerous sect in the country, estimated at 919,000, or 41 percent of the population.

Shias of Lebanon, most of whom were Twelver or Imami Shias, lacked their own state-recognized religious institutions, independent of Sunni Muslim institutions, until 1968 when Imam Musa as Sadr, an Iranian-born cleric, created the Higher Shia Islamic Council. Sadr was elected chairman of the council, which was supposed to represent Lebanese Shias both at the political and religious levels. The council included as members all Shia clerics, as well as deputies, state employees, ministers, writers, professionals, and most noted Shias residing in Lebanon.

Sadr, as chairman for life, continued to head the council until 1978, when he "disappeared" in Libya while on a state visit. He reportedly was kidnapped and killed by Libyan authorities for unknown reasons. Shia leaders in Lebanon as of 1987 still refused to acknowledge Sadr's death. While the chairmanship of the council was preserved for Sadr's awaited "return," in 1987 Shaykh Muhammad Mahdi Shams ad Din (also seen as Chamseddine) was the vice chairman of the Higher Shia Islamic Council. Moreover, a new Shia leader emerged in the early 1980s in Lebanon. Shaykh Muhammad Husayn Fadlallah, the spiritual guide of Hizballah (Party of God), became the most important religious and political leader among Lebanon's Shias.