- Background Currently available TMS stimulators have a single channel operating a single coil. Objective To outline and present physical and physiological benefits of a novel convenient multi-channel stimulator, comprising five channels, where the stimulation parameters of each channel are independently controllable. Methods Simultaneous and sequential operation of various channels was tested in healthy volunteers. Paired pulses schemes with various inter-stimulus intervals (ISIs) were studied for the hand APB and the leg AH muscles. Energy consumption and coil heating rates with simultaneous operation of 4 channels was compared to a single figure-8 coil. Results Repetitive operation of separate channels with different stimulation parameters is demonstrated. The operations of various channels can be combined simultaneously or sequentially to induce multiple pulses with ISIs of μs resolution. A universal pattern of inhibition and facilitation as a function of ISI was found, with some dependence on coils configurations and on pulse widths. A strong dependence of the induced inhibition on the relative orientation of the conditioning and test pulses was discovered. The ability of this method to induce inhibition in shallow brain region but not in deeper region, thus focusing the effect in the deep brain region, is demonstrated. A significant saving in energy consumption and a reduction in coil heating were demonstrated for several channels operated simultaneously compared to a standard single channel figure-8 coil. Conclusions The multi-channel stimulator enables the synchronized induction of different excitability modulations to different brain regions using different stimulation patterns in various channels. Multiple pulses operation with coils with various depth profiles can increase the focality of TMS effect in deep brain regions.