Purpose To develop and test a novel method for coil placement in interleaved transcranial magnetic stimulation (TMS)/functional MRI (fMRI) studies.Materials and Methods Initially, a desired TMS coil position at the subject's head is recorded using a neuronavigation system. Subsequently, a custom-made holding device is used for coil placement inside the MR scanner. The parameters of the device corresponding to the prerecorded position are automatically determined from a fast structural image acquired directly before the experiment. The spatial accuracy of our method was verified on a phantom. Finally, in a study on five subjects, the coil was placed above the cortical representation of a hand muscle in M1 and the blood oxygenation level-dependent (BOLD) responses to short repetitive TMS (rTMS) trains were assessed using echo-planar imaging (EPI) recordings.Results The spatial accuracy of our method is in the range of 2.9 ± 1.3 (SD) mm. Motor cortex stimulation resulted in robust BOLD activations in motor- and auditoryrelated brain areas, with the activation in M1 being localized in the hand knob.Conclusion We present a user-friendly method for TMS coil positioning in the MR scanner that exhibits good spatial accuracy and speeds up the setup of the experiment. The motor-cortex study proves the viability of the approach and validates our interleaved TMS/fMRI setup.