Despite great technological progress scientists still are not capable of ascertaining how many species are there on Earth. Systematic studies are not only time-consuming, but sometimes also significantly impeded by constraints of available equipment. One of the methods for morphology evaluation, which is gradually more often used for taxonomical research is microcomputed tomography. It’s great spatial resolution and ability to gather volumetric data during single acquisition without sectioning specimen are properties especially useful in evaluation of small invertebrates. Nondestructive nature of micro-CT gives possibility to combine it with other imaging techniques even for single specimen. Moreover, in case of rare organisms studies it allows to collect full structural data without fracturing their bodies. Application of proper staining, exposure parameters or specific sample preparation significantly improves quality of performed studies. The following article presents summary of current trends and possibilities of microtomography in morphology studies of small invertebrates.