AbstractLongitudinal analyses of magnetoencephalography (MEG) data are essential for a full understanding of the pathophysiology of brain diseases and the development of brain activity over time. However, time-dependent factors, such as the recording environment and the type of MEG recording system may affect such longitudinal analyses. We hypothesized that, using source-space analysis, hardware and software differences between two recordings systems may be overcome, with the aim of finding consistent neurophysiological results. We studied eight healthy subjects who underwent three consecutive MEG recordings over 7 years, using two different MEG recordings systems; a 151-channel VSM-CTF system for the first two time points and a 306-channel Elekta Vectorview system for the third time point. We assessed the within (longitudinal) and between-subject (cross-sectional) consistency of power spectra and functional connectivity matrices. Consistency of within-subject spectral power and functional connectivity matrices was good and was not significantly different when using different MEG recording systems as compared to using the same system. Importantly, we confirmed that within-subject consistency values were higher than between-subject values. We demonstrated consistent neurophysiological findings in healthy subjects over a time span of seven years, despite using data recorded on different MEG systems and different implementations of the analysis pipeline.