Within our research project, 34 river bottom sediments were collected in 2006–2007 at five areas across Slovakia with industrial sources of persistent organic pollutants (Košice, Krompachy, Nemecká, Šala, Nováky) and one background area (Starina). Sediments were analyzed for seven 2,3,7,8-substituted polychlorinated dibenzo-p-dioxins (PCDDs) and 10 dibenzofurans (PCDFs), 12 dioxin-like and 6 indicator polychlorinated biphenyls (PCBs), hexachlorobenzene (HCB) and 1,1,1,-trichloro-2,2-bis(p-chlorophenyl)ethane (p,p′-DDT) with 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (p,p′-DDE).Analytical procedure based on accelerated solvent extraction followed by a semi-automated clean-up and fractionation was used. Determination of target compounds was performed by HRGC–HRMS analysis.Total WHO toxic equivalent WHO1998-PCDD/F/dl-PCB-TEQ concentrations ranged from 0.26 to 559pgTEQg−1 dry matter (dm), with a median 2.2pgTEQg−1dm. The sums of six indicator PCBs were in the range 0.56–1014ngg−1dm, with a median 11.8ngg−1dm. The concentrations of organochlorine pesticides HCB and p,p′-DDE/DDT varied from 0.15 to 34.8ngg−1dm, with a median 0.91ngg−1dm and 0.46–34.1ngg−1dm, with a median 6.7ngg−1dm, respectively.The most abundant congeners in all sediment samples among dioxins, furans and PCBs were OCDD, 1,2,3,4,6,7,8-HpCDF, PCB-118 and PCB-153.