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A method is proposed for extracting target dipole-source activities from two sets of evoked magnetoencephalographic (MEG) data, one measured using task stimuli and the other using control stimuli. The difference matrix between the two covariance matrices obtained from these two measurements is calculated, and a procedure similar to the MEG-multiple signal classification (MUSIC) algorithm is applied to this difference matrix to extract the target dipole-source configuration. This configuration corresponds to the source-configuration difference between the two measurements. Computer simulation verified the validity of the proposed method. The method was applied to actual evoked-field data obtained from simulated task-and-control experiments. In these measurements, a combination of auditory and somatosensory stimuli was used as the task stimulus and the somatosensory stimulus alone was used as the control stimulus. The proposed covariance difference analysis successfully extracted the target auditory source and eliminated the disturbance from the somatosensory sources.