The mechanical properties of components made of short fibre reinforced composites, generally obtained by injection moulding, are strictly linked to fibre orientation. Therefore, it is of great importance to be able to verify the results of manufacturing process simulations obtained by commercial software. From the experimental point of view, the definition of carbon short fibre structure within a polymeric matrix in a micro-tomography is a non-trivial task, as the X-rays absorption properties of the two phases are very similar. This paper presents how this problem was overcome by using phase contrast imaging techniques. High resolution fibre structure reconstructions could therefore be obtained. The reconstruction of a large sample volume by overlapping of successive tomographies was also discussed. Moreover, this work shows that the anisotropy identification techniques based on morphological parameters, previously introduced by some of the Authors for short glass fibre reinforced polymers, can also be adopted for fibre arrangement identification in this type of materials.