To improve the overall temporal and spatial resolution of brain mapping techniques, in animal models, some attempts have been reported to join electrophysiological methods with functional magnetic resonance imaging (fMRI). However, little attention has been paid to the image artefacts produced by the microelectrodes that compromise the anatomical or functional information of those studies. This work presents a group of simulations and MR images that show the limitations of wire microelectrodes and the potential advantages of silicon technology, in terms of image quality, in MRI environments. Magnetic field perturbations are calculated using a Fourier-based method for platinum (Pt) and tungsten (W) microwires as well as two different silicon technologies. We conclude that image artefacts produced by microelectrodes are highly dependent not only on the magnetic susceptibility of the materials used but also on the size, shape and orientation of the electrodes with respect to the main magnetic field. In addition silicon microelectrodes present better MRI characteristics than metallic microelectrodes. However, metallization layers added to silicon materials can adversely affect the quality of MR images. Therefore only those silicon microelectrodes that minimize the amount of metallic material can be considered MR-compatible and therefore suitable for possible simultaneous fMRI and electrophysiological studies. High resolution gradient echo images acquired at 2 T (TR/TE = 100/15 ms, voxel size = 100 × 100 × 100 µm³) of platinum–iridium (Pt–Ir, 90%–10%) and tungsten microwires show a complete signal loss that covers a volume significantly larger than the actual volume occupied by the microelectrodes: roughly 400 times larger for Pt–Ir and 180 for W, at the tip of the microelectrodes. Similar MR images of a single-shank silicon microelectrode only produce a partial volume effect on the voxels occupied by the probe with less than 50% of signal loss.