The Neurophysiological Biomarker Toolbox (NBT) is an open source Matlab toolbox for the computation and integration of neurophysiological biomarkers (e.g., biomarkers based on EEG or MEG recordings). The NBT toolbox has so far been used in seven peer-reviewed research articles, and has a broad user base of more than 1000 users. The NBT toolbox provides unique features for analysis of resting-state EEG or MEG recordings. NBT offers a pipeline from data storage to statistics including artifact rejection, signal visualization, biomarker computation, statistical testing, and biomarker databasing. NBT allows for easy implementation of new biomarkers, and incorporates an online wiki (the NBTwiki) that aims at facilitating collaboration among NBT users including extensive help and tutorials. The standardised way of data storage and analysis that NBT proposes allow different research projects to merge, compare, or share their data and biomarker algorithms.