Transcranial magnetic stimulation (TMS) is a non-invasive technique used in the treatment of major depression. Meta-analyses have shown that it is more efficient than a placebo and that its efficacy is enhanced by the optimum tuning of stimulation parameters. However, the stimulation target, the dorsolateral prefrontal cortex (DLPFC), is still located using an inaccurate method. In this study, a neuronavigation system was used to perform a comprehensive quantification of target localization errors. We identified and quantified 3 sources of error in the standard method: cap repositioning, interexpert variability in coil positioning and distance between the stimulated point and the expected target. For cap repositioning, the standard deviation was lower than 5 mm in the 3 axes. For interexpert variability in coil positioning, the spatial dispersion of the points was higher than 10 mm in 2 of the 3 axes. For interindividual anatomical variability, the distance between the actual “reference” DLPFC and its standard determination was greater than 20 mm for 54% of the subjects, while one subject out of eleven was correctly targeted which means 10 mm or less from the reference. Results showed that interindividual anatomical variability and interexpert variability were the two main sources of error using the standard method. Results demonstrate that a neuronavigation system is mandatory to conduct reproducible and reliable studies.