The reconfigurable devices - and mainly the FPGA based systems - have been always popular in performance demanding applications, since they are flexible and highly customisable. In such environment it can be quite useful to have a component running an operating system, because it makes possible to develop on a higher abstraction layer, and to communicate with other computers using complex protocols more easily. Linux, which is an open source, well scalable and flexible operating system, is one of the most used in high performance and non-real time applications. In my thesis I have examined how the change of the hardware environment occurring during the normal operation time can be registered in the kernel. This is a typical feature of the reconfigurable devices, as the peripherals in an FPGA can be easily changed any time with a new configuration. The target platform I have chosen is a ZedBoard, which has a Xilinx Zynq-7000 on it. It consists of an FPGA and 2 high performance ARM processor, and this makes it an excellent device for the purpose. The aim of my thesis is to setup a Linux kernel on the Zynq platform and to create a sample project consisting of custom peripherals, drivers and some test applications.