The paired-pulse transcranial magnetic stimulation (TMS) paradigm is increasingly employed to examine intracortical inhibitory processes in different motor tasks. Short-interval intracortical inhibition (SICI) has been shown to vary with the size of the MEP elicited by the test TMS pulse. This suggests that factors that alter MEP size, such as changes in cortical excitability, may confound the interpretation of SICI. However, the effect of excitability on SICI has not been systematically investigated. The present study examined SICI in 11 volunteers. The effect of test TMS intensities ranging from 90 to 150% resting motor threshold (RMT) on SICI was examined in three excitability states in the right first dorsal interosseous muscle: rest, isometric abduction of the left index finger (Contra) and isometric abduction of the right index finger (Active). For all excitability states SICI was not observed when test TMS intensity was less than 110% resting motor threshold. This was true even for the Active condition in which 90 and 100% test TMS intensities elicited large and consistent MEPs. For all conditions moderately suprathreshold test TMS intensities (110-120% RMT) yielded the greatest measure of SICI; increasing test TMS intensities resulted in a progressive reduction in the estimate of SICI. These results suggest that estimates of SICI are systematically affected by the intensity of the test TMS pulse, regardless of excitability state. The results suggest that SICI should be examined using a constant test TMS intensity regardless of changes in cortical excitability and test MEP size.