Abstract The skin is the physical barrier between the fruit and the environment in which it develops. Environmental conditions during fruit development have a large influence on fruit quality, both at the time of harvest and during subsequent storage. It is hypothesised that some features of the skin and sub-epidermal tissues could provide information about the past growing conditions to which the fruit was exposed and therefore be of predictive value for storage quality. In this study, five commercial kiwifruit cultivars (‘Hayward’, ‘Hort16A’, ‘G3’, ‘G9’ and ‘G14’) were studied, and ‘Hayward’ fruit were manipulated during growth with different cultural practices. After harvest at horticultural maturity, X-ray micro computed tomography (μCT) was used to investigate features of the skin and the immediate parenchyma tissue. Despite orchard management practices (crop load and girdling) being observed to effect macro fruit quality parameters (mass, firmness, SSC, and DM), differences in microstructure (e.g. porosity) caused by these practices were not observed. However, porosity and pore size were found to be highly variable between cultivars. The thickness of dense sub-epidermal tissue could be readily measured and the 3-D distribution of raphide bundles was visible as high density particles distributed within the parenchyma. Overall, μCT was found to be a powerful technique to explore fruit epidermal and sub-epidermal structures in three dimensions at a micro level. However, the length of time required for data capture and analysis and the large number of samples required to overcome natural variation within horticultural products need to be considered. Future work may define the impact of differences in porosity or sub-epidermal anatomy on kiwifruit physiology (e.g. firmness change or sensitivity to low oxygen storage atmospheres). With this information, μCT could be used as a screening tool during plant breeding, or to determine the response to agronomic treatments, without conducting lengthy storage trials.