This review presents the neurophysiologic principles and clinical applications of transcranial magnetic stimulation (TMS) and other related techniques of noninvasive cortical stimulation. TMS can serve various purposes for diagnosis or treatment. Regarding diagnosis, TMS is mainly dedicated to the recording of motor evoked potentials (MEPs). MEP recording allows investigation of corticospinal conduction time and cortical motor control in clinical practice. Especially when using image-guided neuronavigation methods, MEP recording is a reliable method to perform functional mapping of muscle representation within the motor cortex. Using various types of paired-pulse paradigms, TMS allows the assessment of brain circuit excitability or plastic changes affecting these circuits. In particular, paired-pulse TMS paradigms are able to appraise the intracortical balance between inhibitory controls mediated by GABAergic neurotransmission and excitatory controls mediated by glutamatergic neurotransmission. Finally, TMS delivered as repetitive trains of stimulation (rTMS) may activate, inhibit, or otherwise interfere with the activity of neuronal cortical networks, depending on stimulus frequency and intensity, and brain-induced electric field configuration. Therefore by modifying brain functions, with after-effects lasting beyond the time of stimulation, rTMS opens exciting perspectives for therapeutic applications, especially in the domain of depression and chronic pain syndromes.