Transcranial magnetic stimulation (TMS) is a non-invasive tool for electrical stimulation of nervous system. TMS is an effective technology with potential diagnostic and therapeutic uses in various diseases. TMS can be applied as single pulses of stimulation, paired-pulse, or in trains, repetitive TMS. In this survey we try to cover some important areas, such as biological effects, the safety issues, contraindications on TMS. According to available evidence, TMS could be an effective method for improving functional recovery of stroke patients. rTMS was able to improved motor function in the hemiplegic side, poststroke aphasia, manual dexterity and has a promising potential in neuromodulation of autonomic nervous system. Moreover repetitive TMS might become useful in the rehabilitation of patients with dementia in the attempt to restore impaired brain plasticity. The main deficiency of rTMS is that it has no long-lasting effect on motor function in patients with stroke. Creating a home device to deliver TMS can be an important step in rehabilitating the patients with stroke. All these are supported by the available studies, but more investigations are needed to establish the clinical indication as a diagnostic or therapeutic tool in any neurological or psychiatric disease.