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This paper describes a solution for the gradual migration to Linux OS of the MS Windows based IT infrastructure. Planned according to the customer demands, the migration is workstation oriented while the network and server infrastructure remain based on Microsoft technologies. The user applications (MS Windows, Java and Web based) and local peripherals (readers, printers etc.) should remain unchanged and fully functional. Presented solution is based on application virtualization with three methods: virtual machine, Citrix Presentation server or Wine emulator. Workstations are configured and installed in a standardized manner in order to be relocatable by using disk images. All shared network resources can be used by the workstations and the majority of applications is installed on intranet servers. Users and asset management is accomplished through the MS Active Directory service which is used in the infrastructure. Installed Linux OS was enhanced with new developed program which assure that the local peripherals can be used by the virtualized applications. The migration was performed with several workstations of different hardware configurations and tested in everyday operation. Hardware and software compatibility with the previous MS Windows workstation is maintained while the stability and security of the whole infrastructure is increased.