This paper analyzes the main intuition behind Regional Innovation System (RIS). The aspects that are the reasons of regional disparities in terms of innovation, such as clusters, agglomerations, research and development (R&D) will be investigated. Aligned with these aspects this paper will try to analyze the reasons for these disparities between regions. As the final part of step one, policy approaches and innovation strategies towards the regions that are distinguished due to disparities (as, peripheral, metropolitan and industrial regions) will be presented. The second step will constitute of the analysis of Turkey's, Aegean, Marmara, East Anatolia and Southeast Anatolia regions with respect to the results reached in the first step. The policy applications regarding regional innovation systems, the effects of universities in the mentioned regions and the adopted policies within the process of EU membership, are going to be presented. In the final part, the RIS policy implications and their effects and drawbacks in Turkey will be summarized.