Commemorations will centre on the mosque at Qom
Religious seminaries across Iran are closed on Wednesday in memory of scores of Shia clerics killed by the Iraqi regime.
Around 180 senior religious leaders, more than half of them thought to be Iranian, were killed by the Baathist regime.
On Sunday the Supreme Leader, Ayatollah Khamenei, gave his condolences to the families of those killed by Saddam Hussein and called on the enemies of Islam to be destroyed.
The day of mourning is centred in the holy city of Qom, home to thousands of Iraqi clerics who fled there during Saddam Hussein's reign.
They are gathering at the city's main seminary before heading towards the Grand Mosque to attend a ceremony.
Now that the Baathist regime in Iraq has been toppled, most of the Iraqi clerics who came to Iran are expected to return to their communities in Najaf and Karbala, previously seen as the world centres of Shia Islam.
Imam Ali, the son-in-law of the Prophet Mohammed, is buried in Najaf.
Although the Shias of Iran and Iraq have enjoyed close relations over the years, it is not clear if they agree on the nature of Iraq's future style of government.
Sources close to Iraqi clerics in Qom say most of them do not support the Iranian system of Velayet-e-Faqih, which gives the country's top religious leader the ultimate authority in running the affairs of the state.
Instead they believe religion and politics should be separate.
Some have even said the interference of religion in politics has damaged Islam and undermined the faith.
The expected revival of Najaf will be watched closely by Iran's conservative clerics.
Many fear a secular Iraq could pose a threat to their rule.