Transcranial magnetic stimulation is investigated as a new tool in the therapy of depression and other psychiatric disorders. In almost all studies, the dorsolateral prefrontal cortex (DLPFC) has been selected as the target site for stimulation. Usually this region was determined by identifying the patient's motor cortex, and from there the coil was placed 5 cm rostrally. The aim of our study was to test the reliability of this standard procedure. A neuronavigational system was used to relate the final coil position after applying the standard procedure to the individual cortical anatomy. In 7 of 22 subjects, the Brodman area 9 of the DLPFC was targeted correctly in this manner. In 15 subjects, the center of the coil was found to be located more dorsally (e.g., above the premotor cortex). The current method for locating the DLPFC is not precise anatomically and may be improved by navigating procedures taking individual anatomy into account.