A system, method and computer program product for system for detecting a rootkit on a computer having an operating system, including a native application in ring 0 which, when the operating system is in a trusted state upon a reboot of the computer, after loading of the boot drivers but before loading of non-boot drivers, generates a first snapshot for selected files of the operating system and for a registry; the first snapshot being stored on a persistent storage medium of the computer; a second snapshot for the selected files and for the registry generated by the ordinary application after the loading of the non-boot drivers, generating; means for comparing the second snapshot with the first snapshot; and upon detecting, in the comparing step, one of a masked file and a masked registry branch, means for informing a user of possible rootkit presence on the computer.