For more than a decade, Magnetic Resonance Imaging (MRI) has been routinely employed in clinical diagnostics because it allows to non-invasively study anatomical structures and physiological processes in vivo and to differentiate between healthy and pathological states, particularly in soft tissue. Here, we demonstrate that MRI can likewise be applied to fossilized biological samples and help in elucidating paleopathological and paleoecological questions: Five anomalous guards of Jurassic and Cretaceous belemnites are presented along with putative paleopathological scenarios directly derived from 3D Magnetic Resonance images with microscopic resolution. These syn vivo deformities of both the mineralized internal rostrum and the surrounding former soft tissue can be traced back in part to traumatic events of predator-prey-interactions, and partly to parasitism. Evidence is presented that the frequently observed anomalous apical collar might be indicative of an inflammatory disease. Finally, the potential of Magnetic Resonance techniques for further paleontological applications is being discussed.