Microplastic (MP) contamination represents a growing environmental and biological concern, yet the fate and transport of MPs within living organisms remain insufficiently understood. Micro-computed tomography (μCT) offers a novel non-destructive approach for three-dimensional visualisation and localisation of particles in intact biological tissues, overcoming the limitations of conventional analytical methods that require destructive sample preparation and lack spatial information. This doctoral thesis systematically investigates the potential of μCT for the detection and tracking of MPs in biological samples, with a focus on Danio rerio as a model organism. A non-destructive workflow was developed for the visualisation and localisation of MPs in intact fish and extracted intestines. Using spherical polyethylene MPs for methodological validation, practical detection limits were established, and reliable spatial mapping of particles within the digestive tract was demonstrated. The developed approach further enabled three-dimensional tracking of ingested MPs and analysis of their transport, retention, and elimination over time. To increase environmental relevance and preliminarily assess the influence of particle shape and material properties on detectability, MPs of various shapes and selected polymers differing in density and additive content were included in the analysis. As establishing detection limits for all MP types and shapes would require a substantially more extensive effort beyond the scope of this work, a procedure for the systematic determination of these limits was proposed. This work establishes μCT as a powerful complementary technique for MP research, enabling non-destructive, spatially resolved detection and tracking of particles within intact organisms. By preserving anatomical context and allowing temporal analysis of ingestion and elimination, the developed methodology provides information that is inaccessible through conventional MP detection methods and opens new opportunities for studying the internal fate and biological interactions of MPs.