BACKGROUND Non-invasive brain stimulation methods such as transcranial magnetic stimulation (TMS) are starting to be widely used to make causality-based inferences about brain-behavior interactions. Moreover, TMS-based clinical applications are under development to treat specific neurological or psychiatric conditions, such as depression, dystonia, pain, tinnitus and the sequels of stroke, among others. BACKGROUND TMS works by inducing non-invasively electric currents in localized cortical regions thus modulating their activity levels according to settings, such as frequency, number of pulses, train and regime duration and intertrain intervals. For instance, it is known for the motor cortex that low frequency or continuous patterns of TMS pulses tend to depress local activity whereas high frequency and discontinuous TMS patterns tend to enhance it. Additionally, local cortical effects of TMS can result in dramatic patterns in distant brain regions. These distant effects are mediated via anatomical connectivity in a magnitude that depends on the efficiency and sign of such connections. CONCLUSIONS An efficient use of TMS in both fields requires however, a deep understanding of its operational principles, its risks, its potential and limitations. In this article, we will briefly present the principles through which non-invasive brain stimulation methods, and in particular TMS, operate. CONCLUSIONS Readers will be provided with fundamental information needed to critically discuss TMS studies and design hypothesis-driven TMS applications for cognitive and clinical neuroscience research.