Zebrafish and other small laboratory fish have emerged as important model systems for bone biomedical research. Micro-computed tomography (microCT) is a powerful approach to non-destructively visualize and quantify bone morphology, microarchitecture, and mineral density. While consensus methods for microCT scanning analysis have been established in other vertebrates including small rodents, the small size of zebrafish, their different anatomy, and their amenability to rapid-throughput and high-content approaches call for unique considerations. In this chapter, we describe key considerations for performing microCT scans in the zebrafish skeleton. We also describe different approaches for sample mounting, scan acquisition, and analysis that can be used depending on experimental objectives and outcomes. Finally, we describe a step-by-step protocol for microCT scanning and analysis of adult zebrafish using FishCuT, resulting in hundreds of descriptors of vertebral morphology and mineral density.