: Cork is a natural cellular material with a rather unique set of properties, and its best known application is as stopper for wine bottles. The cork tissue contains structural discontinuities, for example, lenticular channels (LCh), that influence the in-use performance of cork products. X-ray microtomography, in combination with image analysis, has been used for cork characterisation and provided new insights into the three-dimensional location of discontinuities, which are hidden for a visual inspection. It was demonstrated that the presence of LCh is positively correlated with cork density, and the void fraction of LCh in the lower part of a cork stopper is strongly related to the oxygen ingress in the bottle during the first month after bottling. The results contribute to better understanding the natural variation of cork properties.