The behavior of magnetic particles inside elastomeric matrices is a complex issue and can be influenced in many ways, e.g. by applying a magnetic field or external mechanical stimuli. It is of fundamental interest for theoretical descriptions and technological applications to study processes like structure formation of these particles in a magnetic field. For a better understanding of the microstructure and the motion of particles in magnetorheological elastomers (MRE), x-ray micro-computed tomography (Xμ-CT) investigations were carried out. A MRE with a quantity of 2 wt.% of iron powder and an isotropic allocation of the particles inside the matrix was prepared. By means of quantitative analysis with image processing software, information regarding the geometrical properties of the particles and their individual motion under the influence of a magnetic field was obtained. Therefore a set of three tomograms—a reference taken without magnetic field, a second tomogram in presence of an applied field and third one again taken at B = 0 mT—has been taken and compared. It is shown that the combination of Xμ-CT and digital image processing provides a tool for a quantitative analysis of single particle motion in a MRE forced by external stimuli.