Transcranial magnetic stimulation (TMS) is currently used for cognitive studies and investigated as a treatment for psychiatric disorders. Because of the cortex variability, the coil positioning stage is difficult and should be improved by using individual neuroimaging data. Sophisticated and expensive neuronavigation systems have been developed to guide the coil to selected regions on the patient's magnetic resonance images (MRI). Our objective was to develop a triangulation-based MRI-guided method to position manually the TMS coil over the subject's head, using a cortical target derived from individual MR data. We evaluated both the spatial accuracy and the reproducibility of the method using functional MR activations of two different targets in the motor and parietal cortices. The accuracy of the MRI-guided method, assessed from the Euclidean distance (D(m)) between the thumb motor target and the coil position eliciting reproducible thumb motor-evoked potentials with TMS, was D(m) = 10 +/- 3 mm. The reproducibility of the method, evaluated across two different operators, was D(m) = 6.7 +/- 1.4 mm for the repositioning in the motor cortex and D(m) = 6.0 +/- 3.2 mm in the parietal cortex. This novel method could be used clinically to assist positioning of the TMS coil.