Toroidal ferrites and magnetic cores are a key part of electromagnetic compatibility (EMC). They are used in several applications as in power converters, low-power supplies, cables, etc. Therefore, it is crucial to properly characterize them for running 3-D simulations. Typically, complex magnetic permeability (CMP) is taken as the main property of the magnetic cores. In this paper the effect of CMP in simulation up to 100 MHz is investigated. The simulation spectrum has been separated into two regions, split by the resonance frequency, and simulations of several 3-D models with different CMP values are compared with their measurements in each of the regions. Three different magnetic cores are studied: two of them are used for common-mode chokes, while the other is used for interference suppression in wires. With regard to the material, two of them are ferrite cores while the other one is a nanocristalline core. Results show the major importance of CMP in 3-D simulation. However, above the resonance frequency, modeling with only CMP is not valid and other core-related effects as electric permittivity or conductivity must be considered.