Microstructural defects (more precisely their size, their distribution, and their intrinsic characteristics) are known to have a strong impact on crack initiation and propagation and therefore on the material durability. Ultimately, X-Ray tomography represents a relevant experimental tool to provide a 3D characterization of these material defects descriptors. However, the interest of this technique still needs to be evaluated when using non-synchrotron X-ray source. Moreover, the methodology to extract the pertinent data from the 3D scan need to be optimized, especially when phase contrast in the materials is small, as it is the case between carbon black filler and the polymer matrix. In this work, an EPDM matrix is filled with ZnO, Carbon Blacks and Calcium carbonates so that different possible source of structural defects can be evaluated. Several model materials with controlled defects concentration and distribution are then processed. In details, various statistical information such as the distributions of the size and of the inter-particle distance for these defects are computed based on laboratory X-ray Tomography measurements. The discussion then focuses on methodology to determine these crucial microstructural parameters.