This paper presents a computational fluid dynamic analysis of a small-scale commercial biomass pellet boiler. Combustion of the particles in the bed plays a key role in the analysis of this kind of systems, and a stand-alone code was used in this work to provide the inlet conditions for the CFD analysis. Model predictions were compared with the experimental gas temperature and species concentration measurements, which were in good agreement. On the basis of the CFD analysis it can be concluded that the interaction of the particles in the bed and the poor mixing of the gases in the furnace are the key factors leading to the high emission levels that are typical of small-scale systems.