The capacity to externally control transcranial magnetic stimulation (TMS) devices is becoming increasingly important in brain stimulation research. Here we introduce MAGIC (MAGnetic stimulator Interface Controller), an open-source MATLAB toolbox for controlling Magstim and MagVenture stimulators. MAGIC includes a series of MATLAB functions which allow the user to arm/disarm the stimulator, send triggers, change stimulator settings such as amplitude, interpulse intervals, and frequency, and receive stimulator setting information via a serial port connection between a computer and the stimulator. By providing external control capability, MAGIC enables greater flexibility in designing research protocols which require trial-by-trial changes of device settings to realize a priori trial randomization or interactive ad hoc adjustment of parameters during an ongoing experiment. MAGIC thus helps to prevent experimental confounds related to the block-wise variation of parameters and facilitates the integration of TMS with cognitive/sensory tasks, and the development of more adaptive brain state-dependent brain stimulation protocols.