The differences in the pollutant emissions from the combustion of bituminous coal and biofuels (wood, straw, and miscanthus pellets) under real-world boiler operating conditions were investigated. The experiments were performed on an experimental installation that comprised an 18 kW boiler, used in domestic central heating systems, equipped with a retort furnace, an automatic fuel feeder, a combustion air fan, and a fuel storage bin. The emission factors of gaseous pollutants, particulate matter, organic carbon, elemental carbon, and polycyclic aromatic hydrocarbons (PAHs), as well as some PAH concentration ratios for coal and biofuel combustion, were determined. The obtained results indicate that fuel properties have a strong influence on the emission factors of gaseous and carbonaceous pollutants. The total particulate matter (PM) emissions from the biofuel combustion were about 5-fold lower than those from the coal burned in the same boiler. The emission factors of the total carbons from the biofuel combustion were between 10 and 20 times lower than those from the coal combustion. The mean organic carbon (OC) and elemental carbon (EC) emission factors, based on the burned fuel, were 161–232 and 42–221 mg/kg for the biofuels and 1264 and 3410 g/kg for the coal, respectively. The obtained results indicate that molecular diagnostic ratios, based on the concentration of PAHs, vary significantly, depending on the fuel type.