Citrus tristeza virus (CTV) is the most important viral pathogen of citrus. CTV-induced stem pitting negatively impacts grapefruit and sweet orange production. The mechanisms of stem pitting development in CTV-infected citrus remain unclear. This study evaluated the utility of high-resolution CT scanning as a tool to study stem pitting in live citrus material. CT scans were used to easily identify pits based on differences in tissue density. Stem pits were also mapped and modelled three-dimensionally along the length of the stem. Nano-CT scanning proved to be a potentially valuable, non-destructive method for stem pitting characterization in citrus.