In this study, pattern electroretinography (PERG) signals were obtained by electrophysiological testing devices from 70 subjects. The group consisted of optic nerve and macular diseases subjects. Characterization and interpretation of the physiological PERG signal was done by principal component analysis (PCA). While the first principal component of data matrix acquired from optic nerve patients represents 67.24% of total variance, the first principal component of the macular patients data matrix represents 76.81% of total variance. The basic differences between the two patient groups were obtained with first principal component, obviously. In addition, the graphic of second principal component vs. first principal component of optic nerve and macular subjects was analyzed. The two patient groups were separated clearly from each other without any hesitation. This research developed an auxiliary system for the interpretation of the PERG signals. The stated results show that the use of PCA of physiological waveforms is presented as a powerful method likely to be incorporated in future medical signal processing. (C) 2006 Elsevier Ltd. All rights reserved.