Intrusion detection is an important technique in the defense-in-depth network security framework and a hot topic in computer security in recent years. In this paper, a new intrusion detection method based on Principle Component Analysis (PCA) with low overhead and high efficiency is presented. System call data and command sequences data are used as information sources to validate the proposed method. The frequencies of individual system calls in a trace and individual commands in a data block are computed and then data column vectors which represent the traces and blocks of the data are formed as data input. PCA is applied to reduce the high dimensional data vectors and distance between a vector and its projection onto the subspace reduced is used for anomaly detection. Experimental results show that the proposed method is promising in terms of detection accuracy, computational expense and implementation for real-time intrusion detection.