This paper will analyze the flotilla crisis in terms of its broader implications for the security perspectives of Turkey and Israel. The crisis, which ensued in the aftermath of the Israeli raid into the Turkish aid convoy on 31 May 2010, has been evaluated as an exception to otherwise good relations between the two countries. I will argue that this crisis should be evaluated within the context of changing security perceptions in the Middle East long in the making. No longer perceiving its neighbors as security threats, Turkey embarked on a road to collide with other countries that base their regional security perception on external threats and enemies. In that sense, we can argue that a "clash of security perceptions" culminated in the flotilla crisis. In this paper, I will attempt to analyze three aspects of Turkey's changed security perception and their implication for the Middle East security: 1) the structural changes that took place in Turkish foreign policy over the past decade, 2) Turkey's increased foreign policy activism in the Middle East, 3) the current state of Turkish-Israeli bi-lateral relationship and its implications for the Middle East.