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<p><strong>Objective</strong> To investigate the feasibility and safety of using navigated transcranial magnetic stimulation (nTMS) to map hand motor cortex and further analyze its clinical application.  <strong>Methods</strong> The first dorsal interosseous (FDI) was selected as target muscle. The location and area of bilateral FDI were mapped by using nTMS in 10 healthy right-handed volunteers. In order to identify the accuracy of nTMS, all individual MRI volumes and the coordinates of hotspots were normalized to Montreal Neurological Institute (MNI) space using SPM8. Positive sites and motor-evoked potential (MEP) were recorded. The areas of hand motor representations were calculated and compared between bilateral cerebral hemispheres.  <strong>Results </strong> nTMS was capable of identifying hand motor cortex area in both hemispheres in all cases. It took 45 to 60 minutes to finish the whole nTMS procedures of each side of hand motor area. The motor cortex was found at the Ω area of bilateral precentral gyri. The right hand motor representation area was significantly larger than that of left area [(6.22 ± 0.76) cm² vs (4.30 ± 0.40) cm²; <em>t</em> = 7.078, <em>P</em> = 0.000]. Four cases presented sleepiness, but no side effect such as headache or epilepsy was found.  <strong>Conclusions</strong> nTMS is a reliable and safe technique to map hand motor cortex. It can be a very useful supplementary tool for preoperative motor cortex mapping and study on motor functional remodeling.</p><p> </p><p><strong>DOI: </strong>10.3969/j.issn.1672-6731.2016.08.011</p>