The three holiest sites in Shia Islam, in descending order, are Masjid al-Haram in Mecca, the Prophet's Mosque in Medina, and Al-Aqsa Mosque Compound in Jerusalem. Beyond this shared recognition across both Sunni and Shia traditions, the two branches place varying degrees of religious and devotional importance on other sites. Twelver Shi'ism is the largest branch of Shia Islam and a major Islamic tradition. In Shia Islam, sites associated with the Imamate hold exceptional significance. Holy cities such as Najaf, Karbala, Mashhad, Kadhimiya, Samarra, Kufa, and Qom are major pilgrimage centers and attract the world's largest numbers of pilgrims annually. The Twelve Imams are also revered in Sunni Islam as family members of Muhammad and as highly important figures in Islamic history, and Sunnis too visit their shrines out of veneration.

Holiest sites accepted by all Muslims

Masjid al-Haram Mecca in Saudi Arabia is the holiest city, as it is the birthplace of Islam, the birthplace Muhammad, and home to the holiest site, Kaaba in Masjid al-Haram. Only Muslims are allowed to enter the city. The rites of hajj pilgrimage is to circumambulate the Kaaba seven times. It contains the Maqam Ibrahim, the Zamzam Well, the hills of Safa and Marwa, Hateem, and the Black Stone, which belonged to Adam and Eve in Paradise. After Abraham built the Kaaba, an angel brought him the Black Stone, a celestial stone that had fallen from Heaven on the Abu Qubays Hill. The Black Stone is believed to be the only remnant of the original structure made by Abraham. After placing the Black Stone in the eastern corner of the Kaaba, Abraham received a revelation in which God told the aged prophet that he should now go and proclaim the pilgrimage to mankind.

Muhammad played a central role in the Kaaba's restoration. Prior to his prophethood, Muhammad was involved in its rebuilding following flood damage in 605 CE, during which he resolved a dispute among Quraysh clans by proposing that the Black Stone be placed on a cloth and lifted collectively, with Muhammad himself setting it in position. After the Conquest of Mecca, Muhammad entered the Kaaba and removed all of its idols, dedicating the house exclusively to the worship of God. He reaffirmed the Kaaba's association with Abraham in Islamic tradition. The area of Mecca also includes Mount Arafat, Mina, Muzdalifah and Jannat al-Mu'alla. As one of the Five Pillars of Islam, every Muslim who is capable must perform the hajj at least once in their lifetime. Hajj is one of the largest annual gatherings in the world, second only to pilgrimages to the Shia Shrines.

The Prophet's Mosque The Prophet's Mosque in Medina, Saudi Arabia, is the second holiest site. Muhammad himself was involved in the mosque's construction. The mosque's land originally belonged to two young orphans, Sahl and Suhayl, and when they learned that Muhammad wished to acquire their land to build a mosque, they went to him and offered the land as a gift. Muhammad insisted on paying a price because they were orphaned children. The price agreed upon was paid by Abu Ayyub al-Ansari, who thus became the donor of the mosque on behalf of Muhammad. One of the most notable parts of the mosque is its Green Dome, where Muhammad is buried under it. Originally an open-air building, the mosque served as a community center, a court of law, and a religious school. It contained a raised platform or pulpit (minbar) for the people who taught the Quran and for Muhammad to give the Friday sermon (khutbah). Subsequent Muslim rulers greatly expanded and decorated the mosque. In 1909, under the reign of Ottoman Sultan Abdul Hamid II, it became the first place in the Arabian Peninsula to be provided with electrical lights. It is a tradition to visit the mosque after or before the pilgrimage to Mecca.

The Al-Aqsa Mosque Al-Aqsa Mosque Compound in Jerusalem is where Muhammad ascended bodily into heaven during the night journey (Isra' and Mi'raj), had a vision of afterlife, and returned. It is the third-holiest site, held in esteem by both Sunni and Shia Muslims due to its history as a place of worship by many prophets such as Abraham, David, Solomon, Elijah and Jesus. The compound contains the Dome of the Rock, the Qibli Mosque (Al-Aqsa Mosque), Al-Marwani Mosque and others. Verses 1–18 of Surāh an-Najm of the Quran, and some verses of the Surāh al-’Isrā’, mentions the Al-Aqsa Mosque and allude to the night journey. In 610 CE, Muhammad was taken by angels Gabriel and Michael from Masjid al-Haram in Mecca to visit "The Furthest Mosque" (Masjid al-Aqsa) in Jerusalem over the night, where he led the prayer among the prophets, and was then taken to the heavens from the Foundation Stone.

Shrines of the Imams Najaf Imam Ali Shrine

The Imam Ali Shrine in Najaf, Iraq, contains the tomb of Ali, Muhammad's cousin, his son-in-law, and the first Shia Imam. The shrine's significance and holiness is profound. All Muslims revere Ali, but the Shia in particular, as a paragon of justice, knowledge, and piety. As the burial site of one of Islam's most important figures, the Imam Ali Shrine is considered by Shia Muslims as the holiest site in Islam after Mecca, Medina, and Jerusalem. The Quran contains numerous debatable references to Ali, including in the Verse of walaya, Laylat al-mabit, and Verse of Ikmal ad-Din. Numerous sayings of Muhammad highly praise Ali. The Hadith of the Position, attributed to Muhammad, equates the standing of Ali to him with the standing of Aaron to Moses. Muhammad established a pact of brotherhood with him, a distinction he granted to no one else but Ali. Ali played a pivotal role in the early years of Islam, with Sunni Muslims regard Ali as the last of the Rashidun caliphs, while Shia Muslims reveres him as Muhammad’s rightful successor. Every year, millions of pilgrims visit the shrine.

The shrine is surrounded by the world's largest cemetery, Wadi al-Salam. It is believed that being buried near Ali brings spiritual benefits, and many request to be interred in this sacred ground.Robert Fisk, "The Largest Cemetery on Earth", The Independent, 2008. Ali was buried in Najaf following his assassination. Before his death, Ali instructed his sons, Hasan and Husayn, regarding the location of his burial. In accordance with his wish, Ali's grave was kept secret, and its location was known only to the Shia Imams. This was to protect his grave from desecration by the Kharijites. His grave remained a closely-guarded secret for over a century. It wasn't until the 8th century when the grave was revealed by the sixth Shia Imam, Sadiq. It became publicly known during the reign of the Abbasid caliph Harun al-Rashid, after the decline of the Umayyad dynasty and the dispersal of the Kharijites. He built the first structure over the tomb, which included a green dome. Over the centuries, the shrine has undergone numerous expansions. The Buyid dynasty made significant contributions by building a large dome over the grave.Heinz Halm, Shia Islam: From Religion to Revolution, Markus Wiener Publishers, 1997. The Safavid Empire in the 16th century also played a crucial role in further developing the shrine, adding ornate decorations, and expanding the complex.Roger Savory, Iran Under the Safavids, Cambridge University Press, 2007. The shrine is an architectural masterpiece, distinguished by its golden dome and minarets. The central hall, where the tomb is located, is adorned with intricate mirror work, mosaics, and calligraphy.UNESCO, "Heritage of Iraq: Imam Ali Mosque". Many hadiths from the Shia Imams and from Muhammad are about Ali.

Muhammad: "Are you not content, Ali, that you have the same rank with regard to me as Aaron had with regard to Moses, except that there is no prophet after me? There is no sword but Zulfiqar (Ali's sword), and there is no hero but Ali. Whoever visits Ali while he is alive, it is as if he has visited me; and whoever visits him after his death, it is as if he has visited me during my lifetime. I am the city of knowledge, and Ali is its gate."

Karbala Imam Husayn and Al-Abbas Shrines

The holy city of Karbala in Iraq contains the Imam Husayn and Al-Abbas Shrines, two of the profoundly holy sites in Shia Islam. Husayn was the son of Ali, the grandson of Muhammad, and the third Shia Imam. Husayn's shrine stands on the site of his grave, where he was martyred during the Battle of Karbala.Shimoni & Levine, 1974, p. 160.Aghaie, 2004, pp. 10–11. The martyrdom of Husayn and Abbas is commemorated annually by over 20 million Muslims inside Karbala. Up to 34 million pilgrims visit the city to observe Ashura, which marks the anniversary of Husayn's martyrdom. The main event is the Arba'in pilgrimage, where up to 40 million visit the city, the largest annual public gathering on earth. Most of the pilgrims travel on foot and come from all around Iraq and nearly 60 countries. Husayn is a universal, borderless and meta-religion symbol. The Arba'een pilgrimage, while rooted in Shia Islam, has emerged as a symbol of interfaith engagement. It increasingly attracts participants from various religious backgrounds, including Christians, Jews, and non-Abrahamic faiths such as Hindus, Yazidis, and Zoroastrians, who come to commemorate and mourn the martyrdom of Husayn. In addition to Arba'in and Muharram, other significant occasions that draw large crowds to the shrine include the birthdays and martyrdom anniversaries of other Shia Imams.

Husayn, along with his companions and most of his family members, was brutally killed and beheaded by the forces of the Umayyad caliph Yazid. Husayn’s stand against Yazid’s oppressive regime has since been revered as a symbol of resistance and martyrdom. Following the martyrdom, Husayn's grave became a major place of pilgrimage. The first structure over his grave was constructed by the order of al-Mukhtar in the late 7th century.Najam Haider, The Origins of the Shia, Cambridge University Press, 2011. The shrine is renowned for its stunning architecture and intricate decorations, which includes a golden dome, several minarets, and expansive courtyards. The dome is adorned with gold-plated tiles, and the interior features elaborate mirror work, mosaics, and calligraphy that depict verses from the Quran and sayings of Muhammad and the Shia Imams. The shrine also includes a museum that houses objects related to Husayn and the Battle of Karbala, as well as a library. Muhammad reported the events of Karbala on several occasions; For example, he gave a small bottle of soil to Umm Salama and told her that the soil inside the bottle would turn into blood after Husayn was killed. There are narrations that Gabriel informed Muhammad at the time of Husayn's birth that his people would kill Husayn. Several hadiths from the Shia Imams and Muhammad are about Husayn.

Muhammad: "Hasan and Husayn are the masters of the youth of Paradise. Whoever loves them loves me and whoever hates them hates me. Husayn is from me, and I am from Husayn. God loves whoever loves Husayn. Indeed, Husayn is the Lamp of Guidance and the Ark of Salvation."