Anomaly detection is a promising approach to detecting intruders masquerading as valid users (called masqueraders). It creates a user profile and labels any behavior that deviates from the profile as anomalous. In anomaly detection, a challenging task is modeling a user’s dynamic behavior based on sequential data collected from computer systems. In this paper, we propose a novel method, called Eigen co-occurrence matrix (ECM), that models sequences such as UNIX commands and extracts their principal features. We applied the ECM method to a masquerade detection experiment with data from Schonlau et al. We report the results and compare them with results obtained from several conventional methods.