In today’s system design, reconfigurable computing plays more and more an important role. By the extension of reconfigurable devices like FPGAs with one or more CPUs new challenges in system design should be solved. These new hybrid FPGAs (e.g. Virtex-II Pro
), provides a hardcore general-purpose processor (GPP) embedded into a field of programmable gate arrays. Furthermore, they offer partial reconfiguration. Therefore, those hybrid FPGAs are very attractive for implementation of run-time reconfigurable embedded systems. However, most of the efforts in this field were made in order to apply these capabilities at application level, leaving to the Operating System (OS) the provision of the necessary mechanisms to support these applications. In this paper, an approach for run-time reconfigurable Operating System, which takes advantage of the new hybrid FPGAs to reconfigure itself based on online estimation of application demands, is presented. Especially run-time assignment and reconfiguration of OS services over hybrid architecture are discussed. The proposed model uses a 0-1 Integer programming strategy for assigning OS components over hybrid architecture, as well as an alternative heuristic algorithm for it. Furthermore, the evaluation of the reconfiguration costs are presented and discussed.