Most investigations on the internal organization of soft-bodied animals such as cephalopods are based on classical serial sectioning (Le. histological). Here, we demonstrate a state-of-the-art-technique of X-ray microtomography (micro-CT) for 3D imaging of soft-bodied organisms without mineralized structures. As a model, we chose the Hawaiian bobtail squid Euprymna scolopes that is considered a key-organism for study of decabrachiate development While neurodevelopmental as well as gene expression data are available for this species, basic information on its organogenesis is still lacking. We therefore focused our study on major neural ganglia during development, to assess the suitability of micro-CT as non-destructive method for ontogenetic studies. We show that micro-CT in combination with contrast-enhancing substances, such as iodine or phosphotungstic acid, can provide detailed 3D information on the anatomy of cephalopod embryonic structures including the nervous system. The technique eases computer-assisted 3D-reconstructions and modeling due to the perfectly aligned, distortion-free image stacks produced by the micro-CT scans. Non-destructive micro-CT applications have great mapping potential when combined with other classic techniques such as histology, immunocytochemistry, and gene expression studies. (C) 2013 Elsevier B.V. All rights-reserved.