Background: Populations of the European eel (Anguilla anguilla) are declining rapidly and are now considered below safe biological limits. High pollution levels are one of the possible reasons for this decline. Contaminant levels are also of concern with regard to human consumption. This study examined the contamination levels of eels from the North Rhine-Westphalian catchment area of the Rhine and from adjacent rivers. A total of 119 eels from 13 sampling sites were analysed for polychlorinated dibenzo-p-dioxins and furans (PCDD/PCDFs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), mercury, perfluorooctane sulfonate (PFOS) and hexachlorobenzene (HCB). Results: North Rhine-Westphalian eels had very high levels of contaminants comparable to eels from other European water bodies which are strongly influenced by anthropogenic activities. Mean values for PCDD/PCDFs ranged between 0.5 and 5.4 pg WHO 2005 toxicity equivalents (TEQ)/g, for PCDD/PCDF + dl-PCBs between 6.3 and 44.7 pg WHO 2005 TEQ/g, for indicator PCBs between 165 and 1,630 ng/g wet weight (ww), for 6 PBDEs between 9.2 and 242 μg/kg ww, for mercury between 0.069 and 0.314 mg/kg ww, for PFOS between 8.3 and 49 μg/kg ww and for HCB between 3.4 and 50 μg/kg ww. For certain sampling sites, high contamination contents of the eels could be attributed to local sources. Congener patterns for PCBs and PBDEs were described, and biota to suspended matter ratios were calculated. Conclusions: Pollution levels in eels from North Rhine-Westphalia are declining with regard to some contaminants but are still very high. Due to the high contaminant contents, eels from the rivers investigated are not suitable for human consumption. Furthermore, the concentrations of endocrine disrupting contaminants such as PCBs, PCDD/PCDFs and PBDEs in the eels are in a range which might have deleterious effects on the eel populations.