As yet, very little is known about the PCDD/F fate and distribution in the woodchip-fuelled boilers. In this study, the feeding woodchips, stack flue gases and the ashes in different units of a woodchip-fuelled boiler are sampled to investigate their PCDD/F characteristics. The PCDD/F contents in the bottom residues and fly ashes ranged from 18.9 to 66.3 ng I-TEQ/kg, which are below the Taiwanese PCDD/F regulation for reutilization of bottom residues, but still higher than PCDD/F limitations on soils for agricultural use (10 ng I-TEQ/kg), which are adopted by several countries. From the PCDD/F output/input ratios, we found that combustion of woodchips in the boiler system is more favourable for the formations of PCDFs by de novo syntheses, especially for lower chlorinated PCDF congeners. Although about half of the input PCDD/Fs mass are destroyed in the combustion, the output PCDD/Fs toxicity are 6.9 times higher than the inputs. Fly ashes exhibited the highest PCDD/F distributions among the woodchip-fuelled boiler. Still 21.4% of total PCDD/F mass and 18.0% of total PCDD/F toxicity were emitted from the stack flue gases due to the lack of control devices for gaseous phase PCDD/Fs. Decreasing de novo syntheses among the boiler systems, deploying control devices for gaseous phase PCDD/Fs, and proper management on the reutilization of fly ashes will ensure woodchip-fuelled boilers as a sustainable and renewable biomass energy.