Emerging technologies are opening new avenues for the study of past and present ecosystems. Computer-aided visualization and analysis of fossil specimens through X-ray tomography has revolutionized the study of organisms. X-ray tomography, or X-ray computed tomography, is a characterization technique for generating 3D information from 2-dimensional X-ray image slices. X-ray imaging is based on the differential absorption or scattering of an X-ray source to reveal internal attributes of biological specimens. High-resolution tomography can retrieve compositional and structural information of small objects or the macrostructure of larger objects non-destructively, allowing fossils to be characterized in three dimensions and in unprecedented detail. This has enabled paleontologists to gain important insights into the anatomy, development, and preservation of specimens. The resulting digital 3D reconstructions can be used in functional analyses to test hypotheses regarding the paleobiology of extinct organisms that could transform our understanding of long-studied fossil groups, and the narratives of organismal and ecological evolution. Furthermore, this proliferation of digital datasets should make the widespread sharing and dissemination of 3D data possible, providing access to rare fossil material worldwide.