The contents of 49 trace elements in sub-bituminous Pernik coals and their waste products from preparation and combustion processes were investigated. The studied coals have trace element contents higher than the respective Clarke values for brown coals and some of them may pose environmental concerns. The elements Li, Rb, Cs, Ba, Sc, Y, La, Ce, Nd, Sm, Eu, Er, Ga, Zr, Sn, V, Nb, Ta, W, F, Cu, Zn, In, Pb, Cr, Co, Ni, and Th in the feed coals have concentrations that exceed twice the Clarke values. Most element contents in bottom ash are enriched compared with those in feed coal. Some of the volatile elements are equal or significantly depleted including Sn, Mo, Sb, F, Bi, Cd, Ge, and Pb. Fly ash has higher contents of Ga, Zr, Hf, Sn, V, Nb, Mo, and F in comparison with bottom ash. Most elements have a significant positive correlation with ash yield, indicating their inorganic association. The mixed wastes (coal slurry, bottom ash, and fly ash) in the disposal pond are slightly depleted of most of the elements studied with the exclusion of Cl, Ba, and Br. The Pernik coals and their waste products are unpromising for the extraction of REY due to their low element contents.