The Arab Spring changed deeply the political structure of several countries of the Arab world such as Tunisia and Egypt. However, its effects go far beyond the domestic politics of these countries, and are affecting the power balances of the region. The Muslim Brotherhood-linked parties have emerged as a new important player, proposing a new bottom-up approach to power based on an Islamist ideology. Their rise is watched with growing concern by the rich Gulf monarchies that fear the challenge that the Brotherhood may pose in the close future on their monopoly over the political-Islam discourse. Since the 2011 uprisings different tactics to deal with the new “Brotherhood threat” have been adopted by the GCC countries. Some key facts occurred in the end of 2012 have highlighted the differences between the increasingly hostile posture towards the Brotherhood demonstrated by the UAE, Saudi and Kuwaiti authorities, and the Qatari stance. Qatar is emerging as a key supporter of the Muslim Brotherhood in the region, and especially of its most important branch in Egypt. This growing rift among the GCC may result in a new struggle for power within the organization. Saudi Arabia, its traditional leader, may have soon to face the rising power of Qatar and its Brotherhood-linked allies.