A system and method for managing pestware on a protected computer is described. The method in one variation includes monitoring events during a boot sequence of the computer; managing pestware-related events before native applications can run and after a kernel is loaded; managing pestware-related events when native applications can run; and scanning a registry of the computer for pestware when native applications can run. In variations, a pestware management engine is initialized after an operating system of the protected computer is initialized and the pestware management system both receives an event log of the monitored events and compiles the set of behavior rules utilized by kernel-level monitor.