A method for detecting intrusions in the operation of a computer system is disclosed which comprises gathering features from records of normal processes that access the files system of the computer, such as the Windows registry, and generating a probabilistic model of normal computer system usage based on occurrences of said features. The features of a record of a process that accesses the Windows registry are analyzed to determine whether said access to the Windows registry is an anomaly. A system is disclosed, comprising a registry auditing module configured to gather records regarding processes that access the Windows registry; a model generator configured to generate a probabilistic model of normal computer system usage based on records of a plurality of processes that access the Windows registry and that are indicative of normal computer system usage; and a model comparator configured to determine whether the access of the Windows registry is an anomaly.