A subthreshold conditioning stimulation (CS) suppresses the motor-evoked potential (MEP) generated by a test stimulation (TS) at interstimulus intervals (ISIs) of 1–5ms in a paired-pulse transcranial magnetic stimulation (TMS) protocol, a phenomenon termed short interval intracortical inhibition (SICI). Intracortical facilitation (ICF) occurs at ISIs of 7–30ms. Long interval intracortical inhibition (LICI) is elicited with suprathreshold CS preceding the TS at ISIs of 50–200 ms. Previous studies showed that SICI is decreased in the presence of LICI but whether this is due to changes in descending indirect waves (I-waves) induced by LICI or true inhibitory interactions between LICI and SICI has not been resolved. To address this issue, we recorded I-waves in two patients with implanted cervical epidural electrodes and investigated how SICI and ICF changed I-waves in the presence of LICI. SICI alone reduced late I-waves but in the presence of LICI, neither the I-waves nor the MEP were further inhibited by SICI. ICF alone increased MEP amplitude but the I-waves were not facilitated. There was no change of ICF in the presence of LICI compared with ICF alone. We conclude that decreased SICI in the presence of LICI is not due to changes in I-wave content induced by LICI and is caused by their interactions at the cortical level.