We studied the effect of stimulus intensity, coil size, mental alertness and prestimulus muscle contraction on the variability of motor evoked potentials (MEPs) produced by magnetic cortical stimulation (MCS). In 5 healthy subjects we delivered MCS either with a circular coil centered at the vertex or a figure-8 coil centered over the motor cortex hand area, recording from first dorsal interosseous. With the subject at rest or exerting 5% maximum voluntary contraction, 30 consecutive stimuli were given at 4 stimulus intensities (SIs) in 10% increments above resting motor threshold. Concurrent mental arithmetic constituted mental alertness. Spectral analysis was performed on data from 300 consecutive stimuli. The variability of MEP response size was inversely related to stimulus intensity, prestimulus voluntary muscle contraction, the recruitment of motoneurons and the size of the field generated by the magnetic coil. The MEP variability was larger than and not correlated with the variability of the H-reflex. Fast Fourier transformation and cross-correlation analysis did not identify a consistent dominant frequency, suggesting that the variability in MEP size is essentially random. We suggest that the variability in MEP response is caused by constant, rapid, spontaneous fluctuations in corticospinal and segmental motoneuron excitability levels. Any maneuver that raises this level or increases the probability of motoneuron firing will decrease MEP variability.