Introduction TMS has mainly been used- and is often believed to only be suitable for stimulation of superficial cortical areas. However, standard coils have also been used to target deeper volumes, alternatively specially designed coils have been developed for this purpose. We aimed to validate the use of standard coils for the stimulation of deep volumes. We used a system for navigated TMS where the stimulus induced electrical field strength in any location of the brain can be estimated. In the process, we also studied if the use of a midline parieto-occipital location as site for sham-stimulation could be justified. Methods Healthy adults were stimulated using a standard figure-of-eight coil in the Eximia system (Nexstim Ltd). The RMT for activation of the APB and AH muscles on the dominant side were defined. Four scalp locations were stimulated, each with three different intensities in relation to the RMTs: Three scalp locations with shortest Euclidian distance to dACC, insular and hippocampal cortices respectively, one location at the proposed site for sham-stimulation. Results All locations could be stimulated in all subjects. The intensity at the superficial cortical area under the coil, needed to produce sufficient (as compared to the RMTs) electrical field strengths at the deep locations dACC and insula were within a reasonable range (1.5–2 RMT), whereas hippocampal structures were not possible to stimulate using this set up. The sham stimulation location seems to be adequate in terms of not producing significant field strengths over motor cortices. Discussion If navigated stimulation and estimation of electrical field strengths are utilised, a standard TMS setup can be used to stimulate deep structures such as the dACC and insular cortex in a biologically reasonable fashion. A midline parieto-occipital location may be used as a locus for sham-stimulation in studies investigating motor cortex stimulation.