There is currently great interest in replacing fossil-oil with renewable fuels in energy production. Fast pyrolysis bio-oil (FPBO) made of lignocellulosic biomass is one such alternative to replace fossil oil, such as heavy fuel oil (HFO), in energy boilers. However, it is not known how this fuel change will alter the quantity and quality of emissions affecting human health. In this work, particulate emissions from a real-scale commercially operated FPBO boiler plant are characterized, including extensive physico-chemical and toxicological analyses. These are then compared to emission characteristics of heavy fuel-oil and wood fired boilers. Finally, the effects of the fuel choice on the emissions, their potential health effects and the requirements for flue gas cleaning in small-to medium-sized boiler units are discussed. The total suspended particulate matter and fine particulate matter (PM) concentrations in FPBO boiler flue gases before filtration were higher than in HFO boilers and lower or on a level similar to wood-fired grate boilers. FPBO particles consisted mainly of ash species and contained less polycyclic aromatic hydrocarbons (PAH) and heavy metals than had previously been measured from HFO combustion. This feature was clearly reflected in the toxicological properties of FPBO particle emissions, which showed less acute toxicity effects on the cell line than HFO combustion particles. The electrostatic precipitator used in the boiler plant efficiently removed flue gas particles of all sizes. Only minor differences in the toxicological properties of particles upstream and downstream of the electrostatic precipitator were observed, when the same particulate mass from both situations was given to the cells.