Source localization based on magnetoencephalographic and electroencephalographic data requires knowledge of the conductivity values of the head. The aim of this paper is to examine the influence of compartment conductivity changes on the neuromagnetic field and the electric scalp potential for the widely used three compartment boundary element models. Both the analysis of measurement data and the simulations with dipoles distributed in the brain produced two significant results. First, we found the electric potentials to be approximately one order of magnitude more sensitive to conductivity changes than the magnetic fields. This was valid for the field and potential topology (and hence dipole localization), and for the amplitude (and hence dipole strength). Second, changes in brain compartment conductivity yield the lowest change in the electric potentials topology (and hence dipole localization), but a very strong change in the amplitude (and hence in the dipole strength). We conclude that for the magnetic fields the influence of compartment conductivity changes is not important in terms of dipole localization and strength estimation. For the electric potentials however, both dipole localization and strength estimation are significantly influenced by the compartment conductivity.