The different types of magnetic stimulators available commercially permit preferential activation of an area of cortex confined to one hemisphere. Stimulating bilaterally may be a desirable means, however, of obtaining information from each hemisphere simultaneously at rest or during a motor task. The aims of this study were to validate and optimize this method by comparing the biophysical and the physiologic features of biphasic with monophasic stimulation from a circular coil. Five (three male, four right-handed) healthy adults were studied. Relaxed proximal and distal upper limb muscles were activated using a 13-cm outer diameter circular coil centered at the vertex. Motor evoked potentials (MEPs) were recorded simultaneously and bilaterally from the abductor pollicis brevis and from the biceps. Stimulators were used to generate different induced pulse waveforms (biphasic or monophasic), which were calibrated in volts. Stimulus-response (S/R) curves were then constructed by adjusting the intensity of stimulation in 10% increments. The datasets were then modeled using a linear function. Biphasic stimulation, with the first phase of coil current being counterclockwise when viewed from above, produced comparable S/R curves to monophasic stimulation with no significant difference in grouped data ( > 0.5 for abductor pollicis brevis and > 0.07 for biceps). Individually there was a tendency for biphasic MEPs to be larger in amplitude compared with monophasic MEPs. Bilateral stimulation produced MEPs of comparable shape and latency with the biphasic protocol. Right- and left-side S/R curves can be constructed simultaneously from selected proximal and distal upper limb muscles groups by using a centered circular coil delivering a biphasic pulse.