Nowadays, additive manufacturing techniques such as the Fused Filament Fabrication appear to be among the most promising methods for enabling modern industry to produce components of high geometrical complexity. The main characteristic of this method is the deposition of thermoplastic polymers that can be further reinforced with chopped and/or continuous fibers that attribute to the product some unique structural characteristics. Nevertheless, the process is susceptible to a variety of defects that are derived from the fabrication process parameters, such as porosity, insufficient fiber impregnation with the polymer and fiber disorientation. On the other hand, since the applicability of the process depends on the development of numerical tools for assessing the effects of these defects, the accurate detection and quantification of them is a crucial part of it. In the present work, these defects are studied experimentally by implementing an X-ray computed tomography testing campaign. The manufacturing defects are identified using well-established techniques while a complete analysis of the distribution of porosity is presented for various zones of Onyx, Onyx/Carbon and Onyx/Glass fiber reinforced structures. Finally, the tendency of the overall pore content to increase with increasing number of continuous fiber reinforcement was identified as well as porosity variations in printing direction are presented.