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We describe an electroencephalographic (EEG) device and protocol that allows recording of electrophysiological signals generated by the human brain during transcranial magnetic stimulation (TMS) despite the TMS-induced high-voltage artifacts. The key hardware components include slew-rate limited preamplifiers to prevent saturation of the EEG system due to TMS. The protocol involves artifact subtraction to isolate the electrophysiological signals from residual TMS-induced contaminations. The TMS compatibility of the protocol is illustrated with examples of two data sets demonstrating the feasibility of the approach in the single-pulse TMS design, as well as during repetitive TMS. Our data show that both high-amplitude potentials evoked by visual checkerboard stimulation and low-amplitude steady-state oscillations induced by auditory click-trains can be retrieved with the present protocol. The signals recorded during TMS perfectly matched control EEG responses to the same visual and auditory stimuli. The main field of application of the present protocol is in cognitive neuroscience complementing behavioral studies that use TMS to induce transient, 'virtual lesions'. Combined EEG-TMS techniques provide neuroscientists with a unique method to test hypothesis on functional connectivity, as well as on mechanisms of functional orchestration, reorganization, and plasticity.