Rare earth element (REE) concentrations in coals are a source of information relevant to the evolution of source rocks, depositional environment, and epigenetic tectonic activity as well as the effects of igneous intrusions. In this study, 186 coal samples, 11 intrusion-affected coal samples, 4 samples representative of the intrusive rocks, one coal roof and one parting samples were collected from 29 boreholes at the Zhuji coal mine, Huainan Coalfield, Anhui Province, China. The main objective is to characterize the intrusive rocks in the coal-bearing sequence and to investigate the correlation of REE parameters in the coals with the source rocks, depositional environment, localized faults, igneous intrusions, and thickness of the coal beds. A sequence (from base to top) of acidic to basic intrusive rocks through the coal-bearing strata was identified, which possibly corresponds to different intrusive episodes of granite, diorite/monzonite and gabbro. Both the REE contents and degree of fractionation of light rare earth elements (LREE) and heavy rare earth elements (HREE) increase from acidic to basic rocks. Most rocks are slightly depleted in Ce but highly depleted in Eu. The REE concentrations in coals from the Zhuiji mine (average of 118 mu g/g) are nearly identical to recently-updated average Chinese values, but significantly higher than global values. The REE content of the intrusion-affected coals is not distinctively different from that of the other coals (P = 0.2), and REE concentrations of the igneous rocks appear to have no clear relationship to those of the intrusion-affected coals. The depositional environment and source rocks are presumably the main REE contributors to the coal-accumulation basin. The REE content in coals from fault-affected boreholes is higher than that in other boreholes and this trend is stronger in the coal seams of the upper strata. The HREE tend to be incorporated into thinner coal seams and the degree of fractionation between LREE and HREE of the coal-forming materials increases with coal thickness.