Transcranial magnetic stimulation (TMS) is a method based on the excitation of neurons in the brain cortex by an alternating magnetic field. Repetitive TMS (rTMS) is a kind of stimulation, in which a series of pulses are generated. rTMS can modulate different cortical area’s activity and change their interactions using different protocols. The review shows the application of rTMS in treatment of various neurological (stroke, Parkinson’s disease, dystonia, chronic pain syndromes, tinnitus, epilepsy, spasticity syndrome) and psychiatric (depression and anxiety) disorders. Authors collected all the main protocols, and gave recommendations for their use in clinical practice according to principles of evidence medicine.