Forests are a well-known carbon sink, which mitigate the rise in atmospheric CO₂ and hence global warming. However, methane emissions by stems of living trees become a major concern due to the increasing contribution of methane to global warming. There are growing evidences that some trees produce methane in their stem. While the final goal will be to upscale tree CH₄ emissions to the ecosystem and regional levels, we first need to understand how heartwood production and trunk emission are related. Measurements were made in the Ashiu Experimental Forest on two to five trees of 13 species and at two positions along the trunk. Several species at this site have the potential to produce CH₄ in their heartwood and harbour methanogenic archaea. However, only some of them significantly emitted CH₄ from their stem, while the other, such as sugi (Cryptomeria japonica) exhibited low, or virtually no, CH₄ emission. We postulate that axial transport is favoured at the expense of radial diffusion, especially in species with low volumetric gas fraction in relation to high wood moisture content. Modelling radial and axial gas diffusion is a prerequisite to scale-up tree CH₄ emission at stand level.