In the Iran-Iraq War, one group of those of formal position on the war was the clergies and religious scholars in Qom and Najaf. Undoubtedly, the religious leadership of Shi'a Muslims in both countries and their position could have played an important role in the reaction of their followers and the success or failure of each side of the war. The present study seeks to compare the positions of clergymen in the Qom and Najaf center of religious sciences in the Iran-Iraq war. The findings of this study show that, contrary to the full support of clergies in Qom for the Iranian warriors and their persuasion to defend the country, those in Najaf opposed their regime's invasion of neighboring Muslim countries. Of course, they differed in terms of the way of opposition. Some opposed the Ba'ath regime and its military actions, but some remained silent, despite their desire.