The fact that the government felt compelled to treat the grandson of Ayatollah Khomeini and two grand ayatollahs as enemies of the state shows how worried the regime is about its religious authority. It is likely that further humiliation will be directed at other dissident clerics.

The new conflict between Khamenei and conservative clerics is not about the legitimacy of the theory of velayat-e-faqih — these clerics believe in that concept. It is about how Khamenei has reached far beyond the powers he is entitled to as supreme leader.

In fact, a large segment of the clerical population does not believe in the theory of velayat-e-faqih and thinks the clergy should stay away from politics. One such cleric is the most notable figure in the Shiite world, Grand Ayatollah Ali al-Sistani in Iraq, who has many Iranian followers as well. Sistani, along with Ayatollah Hossein Kazemeni-Boroujerdi in Iran, for example, is an adamant supporter of the separation of mosque and state. Boroujerdi, who is currently serving a sentence in Tehran’s notorious Evin prison for his beliefs, thinks that Shiite clerics should not be involved in government.

Although the conflict between Khamenei and the clerics has become a major cause of Iran’s internal crisis, it is often overlooked or misunderstood in the West. The enormous power and influence of the Shiite clergy in Iran is often underestimated because Western governments are focused on Iran’s ability to acquire a nuclear weapon.

Another reason Westerners tend to discount the clerics is due to a perception that Iranians are becoming more secular. This notion is an oversimplification. After 31 years of theocratic rule, there is an increasing tendency in Iran to separate mosque and state. But this does not mean that faith in God and Shiite Islam are evaporating. Religious institutions and symbols are still important to Iranian life.

Khamenei is now facing a unique set of challenges. Conservative clerics, some of whom stand at odds with Ahmadinejad, still enjoy a strong following in Iran. In addition, Khamenei knows his power is not what it was five years ago or on June 11, 2009. The clerical establishment now has the potential to directly challenge Khamenei, which the regime wants to avoid at any cost. Recent attacks against the houses of Montazeri and Sanei made even some senior clerics who are at odds with the reformist clergy angry. They wonder what stops the government from attacking their own homes.

Khamenei’s success is the result of his ability to forge alliances with the Islamic Revolutionary Guards Corps, some clerics, and traditional conservatives. Although his ties to hard-liners and the Revolutionary Guards may seem stronger today, he still needs the support of the clerical establishment.

Khamenei’s idea of the Islamic Republic is certainly less republican and not necessarily more Islamic. With republican institutions in Tehran weakened and his religious authority challenged in Qum, the future of the Islamic Republic and the fate of velayat-e-faqih remain uncertain.