Many human cortical regions are targeted with transcranial magnetic stimulation (TMS). The stimulus intensity used for a certain region is generally based on the motor threshold stimulation intensity determined over the motor cortex (M1). However, it is well known that differences exist in coil-target distance and target site anatomy between cortical regions. These differences may well make the stimulation intensity derived from M1 sub-optimal for other regions. Our goal was to determine in what way the induced electric fields differ between cortical target regions. We used finite element method modeling to calculate the induced electric field for multiple target sites in a realistic head model. The effects on the electric field due to coil-target distance and target site anatomy have been quantified. The results show that a correction based on the distance alone does not correctly adjust the induced electric field for regions other than M1. In addition, a correction based solely on the TMS-induced electric field (primary field) does not suffice. A precise adjustment should include coil-target distance, the secondary field caused by charge accumulation at conductivity discontinuities and the direction of the field relative to the local cerebrospinal fluid–grey matter boundary.