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BACKGROUND Advances in the control of transcranial magnetic stimulation (TMS) have enabled greater randomisation of stimulus intensity. It is unclear if such randomisation improves assessments of corticospinal excitability. NEW METHOD We recorded the amplitude of TMS-induced motor evoked potentials (MEPs) from the first dorsal interosseous muscle of eleven participants, during three TMS protocols: blocks of increasing intensity (IB), randomised blocks (RB) and inter-stimulus randomisation (IR). Stimulus intensities from 90-140% of active motor threshold described corticospinal input-output (I/O) properties. The experiment was repeated in five participants. RESULTS Although MEP amplitudes did not differ between IB, RB and IR stimulation protocols, variability was lowest in the IR protocol, compared to IB and RB protocols. Reliability was highest in the IR protocol, compared to IB and IR protocols. COMPARISON WITH EXISTING METHODS Randomising TMS intensity between each trial produces less variable and more reliable estimates of corticospinal excitability than previously used blocked protocols and produces the same I/O measures. CONCLUSIONS Inter-trial randomization of TMS intensities appears to be the most reliable method for constructing I/O curves at multiple time points and decreases the variability of responses.