Abstract The wettability of wood affects some natural phenomena and applications in industry, such as the ascent of sap in the plant stem, wood drying, and impregnation processes for wood modification. Wettability is generally evaluated by measuring the contact angle using techniques such as the sessile drop method and the Wilhelmy method. However, these methods are not applicable to phenomena at the micro-scale such as liquid transport in hardwood vessels. In this study, micro-CT was used to measure the contact angle of liquid in a single wood vessel directly at the submicron scale. The wettability of a wood vessel was analyzed using contact angles of distilled water and diiodomethane. Conventional contact angles of the wood surface were measured using a fixed drop technique. The average contact angle in a vessel determined by the direct CT observation was significantly smaller than that on the wood surface measured by the sessile drop technique. This discrepancy is attributable to the higher total surface energy of the vessel compared to the free energy of a flat surface. The difference in surface energy is due to different chemical composition distributions in various cell wall layers, roughness and surface topography between the wood surface and vessels, and moisture state.