This thesis deals with the generic detection of bootkits which are relatively a new kind of malicious sofware falling into the category of rootkits. The definition of malicious software is presented along with several examples. Then the attention is paid to the rootkits in the context of Microsoft Windows operating systems. This section lists several techniques used by rootkits. After that, the ways of preventing and detecting rootkits are mentioned. Bootkits are known for infecting hard disks Master Boot Record (MBR). The structure of the MBR is described along with the example of hard disk partitioning. Afterwards, the processor instruction set is outlined and the disassembly of Windows 7 MBR is given. The rest of the thesis is devoted to a description of the course of operating system bootkit infection, bootkit prevention, analysis of infected MBR samples, and in particular to the design, implementation and testing of the generic MBR infection detector.