Background: TMS can directly assess cortical areas, providing a cheaper and faster way to determine the neurophysiological nature of cortical neurons. It becomes a question of whether cortical excitability of dominant and non-dominant hemispheres will have a difference considering that dominant hemispheres have more active motor activation of the dominant hand (1). This study is one of the neurophysiology study series using TMS that was held in RSUD Dr Moewardi using Indonesian population, especially Central Java population, considering other studies are still using the parameter of other races neurophysiology parameter. Objective: To determine the difference in cortical excitability between dominant and non-dominant hemispheres. Method: This research was an observational analytic study. This research was conducted at the Neurorestoration Polyclinic of Dr. Moewardi Regional Hospital from July to August 2019 using a Transcranial Magnetic Stimulation (TMS) tool with neuronavigation. The subject consisted of thirty-two samples that were declared healthy by neurology specialists with right-hand dominance. This study compares cortical excitability through the magnitude of resting motor threshold dominant and nondominant hemispheres using TMS. Statistical analysis used paired T-test with a confidence level of 95% and p <0.05. Results: Subject of the study consisted of 17 male (53%) and 15 female (47%) with 100% dominance of the right hand (left hemisphere). The average ratio of the left and right motor threshold is the same, which is 48%. There is difference in cortical excitability between the left hemisphere and the right hemisphere (p = 0.015; P<0.05). Conclusion: There is a difference in cortical excitability between dominant and non-dominant hemispheres measured by resting motor threshold using TMS