An important goal in current research in the neurosciences is to improve our understanding of the function of neurons. This goal is difficult to reach in humans given the available methods, because especially non-invasive tools lack important spatial resolution that is required to study physiological processes. In our group, we developed an electrophysiological method with which we can non-invasively assess direct (D)- and different indirect (I)-waves from transcranial magnetic stimulation (TMS) applied over the primary motor cortex. These different waves origin from different sites of the corticospinal system, and they enable to estimate changes in corticospinal transmission at the spinal level, changes in the activity of corticospinal output neurons of motor cortex, and changes in the activity of more complex circuits of motor cortex. We will present recent progress in applying our electrophysiological technique to understand physiological mechanisms of paired-pulse and repetitive TMS protocols. We will further discuss how our method can be utilized in future studies to address questions in motor control and pathophysiology.