Since its establishment, the religious regime in Iran has never been able to establish a stable and harmonious relationship between the Shiite seminaries of Qom and Najaf. There is an Iranian concern which surfaces from time to time about the Najaf seminary maintaining its traditional position on velayat-e faqih, which is considered a new opinion in Shiite doctrine. That doctrine was set by the founder of the Iranian revolution, Ayatollah Khomeini, to give his absolute rule a religious basis.

Most of the spiritual references in Qom also do not believe in velayat-e faqih, which makes the Iranian regime apprehensive about the Qom seminary. The two sides also disagree about the methods of governance. The regime's response was to place a number of Qom spiritual references under house arrest and bar them from expressing their views and ideas or continuing their teaching and religious duties.

Even though both seminaries have criticized the regime, there is an especially important disagreement between the regime and Najaf. The latter is located outside Iran, making it more difficult to deal with as compared to Qom. The relationship between the regime and Najaf has gone through three phases: denial, dealing and conflict.

Since its establishment, the Iranian regime has denied the centrality of Najaf in Shiite jurisprudence and considered it to represent a retrograde form of Islam that is non-revolutionary and accommodating. The reasons for this go back to the conflict between Khomeini’s revolutionary approach and the Najafi view, which separates religion and politics. That attitude reached its peak after the death of Sistani’s mentor Sayyid Abu al-Qasim al-Khoei. At the time, Ahmad Jannati, the Friday prayer leader in Tehran, effectively accused Sistani of being accommodating and a traitor by describing him as the “English” reference. Jannati also warned of spiritual references leaving Iran and the danger that this exit will represent to the Islamic regime.