A suite of 72 samples of Illinois Basin coal was collected from 2015 to 2018, from 14 active coal mining and preparation operations in Illinois and Indiana. The goals of the study were to investigate the behavior of trace elements during coal preparation and provide current coal quality data for active mining operations in the Illinois Basin, which has become one of the most important suppliers of U.S. coal. Samples include raw coal, cleaned coal, and waste (refuse) coal. The efficiency of cleaning is shown by reduction of ash yield, increase in heating values, and a pronounced shift in the proportion of sulfur forms. In most raw coals, pyritic sulfur (Py S) exceeds organic sulfur (Org S; Org S/Py S ≤ 1.0), whereas in prepared coals, organic sulfur is the predominant sulfur form (Org S/Py S ≥ 1.0). In waste (refuse) coals, Org S/Py S is substantially reduced, or almost entirely in the pyritic form (Org S/Py S near zero). Trends in the distribution of inorganically-associated lithophile and chalcophile elements are shown, as well those for elements having mixed organic-inorganic associations and those that are primarily organic-hosted. Lithophile elements, including Li, Al, P, Ti, Sc, Rb, Y, Zr, Nb, Cs, Ba, the lanthanides, Hf, Th, and U, are partitioned into waste coals with corresponding reduction in cleaned coals. At the same time, chalcophile elements hosted by pyrite, such as As, Sb, Hg, and Pb, are also partitioned into waste coals. Rare earth elements (REEs), including Sc, Y, and the lanthanides, are enriched in waste coals at levels that approximate their content in the upper continental crust (UCC). Several other critical elements, defined as mineral commodities deemed critical to the economy and security of the United States, including V, Cr, As, Rb, Sb, and Cs, show enrichment in waste coals, that may facilitate their co-extraction with the REEs. Concentrations for elements of environmental concern in cleaned coals are similar to or below those for world average coals with the exception of Pb in coals from Illinois. Laser-ablation ICP-MS (LA-ICP-MS) for pyrite in a subset of 21 samples of raw and cleaned coal provided direct determinations of V, Cr, Mn, Co, Ni, Cu, Zn, As, Se, Mo, Ag, Cd, Sb, Au, Hg, Tl, Pb, and Bi. LA-ICP-MS was used together with bulk sample pyritic sulfur and trace element concentrations to estimate the elemental proportion of bulk Cu, As, Hg, and Pb in pyrite, indicating that Hg and Pb are hosted almost entirely by pyrite, whereas the proportion of Cu and As in pyrite accounts for about half of the bulk content. With growing interest in recovering critical elements from coal, partitioning of a large range of elements into waste coals presents a possible opportunity, but also a potential hazard, due to enrichment in harmful elements such as Hg, As, and Pb.