Differences between control and focal hand dystonia (FHD) subject groups in short interval intracortical inhibition (SICI) as determined by paired transcranial magnetic stimulation (TMS) can be difficult to demonstrate, due to interindividual differences. The purpose of this study was to compare two TMS methods for assessing SICI in 8 control and 7 FHD subjects. Electromyographic (EMG) data were recorded from the first dorsal interosseous (FDI) muscle of the dominant hands of the control subjects and affected hands of the FHD subjects. The first method used a conventional approach of setting conditioning stimulus intensity to 80% of rest threshold (RTh) and test stimulus intensity to 120% RTh. Three interstimulus intervals (ISIs) were used: 2 msec, 3 msec, and the ISI between 2 and 3 msec that produced optimal SICI. The second method was novel in that test stimulus intensity was set to 150% active threshold (ATh), and conditioning stimulus intensity was varied between 50% and 100% ATh. The latter was determined at the threshold for SICI and expressed as a ratio of ATh. There was no difference between the subject groups in the degree of SICI produced using the first method, at the three ISIs studied. However, using the second method, the SICI threshold:ATh ratio was found to be significantly higher for FHD subjects. This finding suggests that determining the SICI threshold:ATh ratio may be a more sensitive measure of intracortical inhibitory function than more conventional methods.