<p>The relationship between brain structure and functional measures, such as resting motor threshold (rMT), is of interest and has been studied in adults, but there is a lack of research in adolescents. We studied the correlation between rMT and the grey matter thickness as well as white matter parameters of the motor cortex, using magnetic resonance imaging and navigated transcranial magnetic stimulation. Forty-five participants (twenty boys and twenty-five girls) aged sixteen to nineteen years were recruited for the study. We determined rMT for the abductor pollicis brevis muscle and investigated the correlation between rMT and grey matter thickness and white matter parameters, fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD) and axial diffusivity (AD) in the hand knob and in the extended hand knob. Grey matter thickness in the primary motor cortex was associated with rMT. We also discovered that white matter parameters RD and MD in a broader area of the primary motor cortex were positively associated with rMT. Both grey and white matter appear to influence cortical excitability in adolescence. Understanding the normal development of the brain is necessary to understand pathological neurodevelopmental processes.</p>