Microbial degradation of a vulcanized natural rubber material treated by a wood decay fungus, Trichaptum abietinum TUES-023 was observed by X-ray μCT with non-destructive 1.25 μm resolution. After treatment with T. abieti num for 172 days at 25 °C in a static condition, the rubber surface distorted and the inside structure became porous due to elution of a filler, calcium carbonate from the rubber. The structural change was observed from subsurface to 328 μm depth in the rubber. In this study, we demonstrate that X-ray μCT have an advantage as a tool to monitor structure of rubber inside without addition of physical damage to the rubber materials.