Magnetic resonance imaging (MRI) is now considered a routine tool for comparative morphological imaging in small vertebrate model organisms. However, the application of high-resolution imaging protocols to visualize the anatomy of invertebrate organisms has not yet become a generally accepted tool among zoologists. Here, we describe MRI protocols that permit visualization of both the internal and the external anatomy of freshly fixed invertebrates and specimens from museum collections. The choice of protocols has been optimized to allow the assembly of the large numbers of datasets that are necessary for comparative morphological analyses. Although the primary focus of our work is on sea urchin internal anatomy, we also present results from a variety of other invertebrate taxa to demonstrate the principal feasibility of MRI studies to obtain anatomical information at high resolutions. Furthermore, we briefly describe procedures suitable for 3D modelling.