X-ray computed tomography (XCT) is an established imaging technique that now is being applied as a novel method for digitalisation of specimens from Natural Collections. This method produces very high-resolution imagery, allowing the reconstruction of the specimen’s body externally and internally. This technique also allows differentiation of hard structures from soft tissue of the scanned macroscopic specimens. However, there have been few attempts to apply this technique to the digitalisation of very small specimens (< 10 mm) like those found in the zooplankton. A further complication for scanning zooplankton specimens is the need for their bodies to be suspended in a liquid medium. Here we present the results from Micro-CT scanning a series of zooplankton specimens of different sizes and with different body structure and composition. Preliminary trials with hard-bodied crustacean zooplankton such as crab zoea and large calanoid copepods were resolved well by this technique. This research constitutes a novel way to digitalise specimens at a resolution as high as 1 micron, leading to the possibility of using the 3D models for taxonomic identification or description of new species. Our results are critical to establishing future digital collections, virtual reality applications, and bio-engineering.