Purpose of this study was to analyze the latency and amplitude of transcranial motor evoked potentials responses from the contralateral and ipsilateral muscle groups to the same stimulus. If responses are because of activation of deeper structures, the latency of both the ipsilateral and the contralateral responses should have no difference. However, a difference in latency would suggest that activation might be occurring at different subcortical levels. Data regarding demographics, medical history, and neurophysiological parameters were collected retrospectively on patients undergoing lumbar spine surgeries. Each side transcranial MEPs was considered as an independent data. Latency and amplitude of motor responses were recorded from the hand muscles of the ipsilateral and contralateral side from the same transcranial stimulus at preincision baseline. Statistical data analysis was performed using SAS 9.4. Paired t test was used to identify mean of differences in latency and amplitude between contralateral and ipsilateral intrinsic hand muscle. Data on 54 patients (104 MEPs) were obtained. Using paired t test, mean of differences in latency between ipsilateral (crossover) and contralateral (desired) intrinsic hand muscle was 0.8967 milliseconds ( P < 0.0001) while median was 0.71 milliseconds. Using paired t test, mean of differences in amplitude between ipsilateral and contralateral hand muscles was -1,071 µV ( P = <0.0001). Significant latency differences were seen between the contralateral and the ipsilateral hand MEP responses using the same transcranial stimulus, suggesting a different subcortical activation. Understanding of this difference might help better in the selection of baselines, and whether to favor responses obtained under the anode or under the cathode.