Over the last few years, a significant increase in the use of alternative fuels in the Polish cement industry has been observed. These are mainly waste and waste-derived fuels. The national leader in this field is Chełm cement plant (Poland), with the share of alternative fuels in the cement kiln heat balance reaching in 2012 the level of 78.5%. In this paper, an analysis of the emission rate of air pollutants from cement clinkering process in the above-mentioned cement plant in the years 1998–2012 was carried out, using the results of continuous and periodic measurements. The compliance with the emission limit values applicable for cement kilns co-incinerating waste was assessed, and the influence of large amounts of burnt alternative fuels on emission of substances such as nitrogen oxides (NOx), sulphur dioxide (SO2), total dust, carbon monoxide (CO), hydrogen chloride (HCl), hydrogen fluoride (HF), total organic carbon (TOC), heavy metals (Hg, Cd, Tl, Sb, As, Pb, Cr, Co, Cu, Mn, Ni and V) as well as polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs).