Conventional visual identification of epileptic spike is a challenging problem in the clinical application of magnetoencephalography (MEG). More importantly, the conventional method has problems of detecting other abnormalities such as high frequency oscillation in the human epileptic brain. The objective of this study was to develop a new approach using magnetic spectral analysis and spatial filtering. Twelve patients with seizure have been studied with a whole cortex MEG system. Fifteen epochs were recorded for each patient; each epoch was 120 seconds. Neuromagnetic spectrum was analyzed using a new method called accumulated spectrogram. Focal increases of spectral power were localized using synthetic aperture magnetometry (SAM). The MEG results were then compared with clinical findings. Focal increases of spectral power have been identified in all patients (12/12, 100%). The locations of the focal increases of spectral power were in agreement with dipole locations of spikes in 9 patients (9/12, 75%). A comparison between MEG results and clinical findings indicated that SAM revealed focal epileptic activities in two patients when dipole fitting failed. The results suggest that epileptic regions could be quantitatively identified and accurately localized using accumulated spectrogram and SAM. In comparison to visual identification of spike, the new approach is objective and sensitive, and provides the possibility of analyzing much wider frequency bands.