Signal processing technology for assessing dynamic system similarity for fault detection and other applications is based on time- and frequency-domain time series analysis techniques and compares the entire autocorrelation structure of a test and reference signal series. The test and reference signals are first subjected to similar pre-processing to help guarantee signal stationarity. Pre-processing may include formation of multivariate signal clusters, filtering and sampling. Multivariate periodograms or autocovariance functions are then calculated for each signal series. Test statistics are computed and assessed to determine the equality of the test and reference signals. When the difference between sample autocovariance functions or periodograms of such signals exceeds a preselected threshold value, fault detection signals and/or related diagnostic information are provided as output to a user.