The Paranaguá Estuarine System (PES) is an important estuarine environment on the Brazilian coast. The economic importance of the PES is mainly related to industries, fuel terminals, and the main South American grain-shipping port. The aim of this work was to determine the vertical distribution of polychlorinated biphenyls (PCBs) in three sediment cores from the PES. The methods included Soxhlet extraction, clean-up, and quantification by gas chromatography with electron capture detection. The concentrations of total PCBs ranged from lower than the detection limit to 6.65 ng g(-1). Low PCB concentrations were detected in P1 and P3, which were collected far away from direct human activities. In P2, the compositional pattern of PCB congeners showed greater concentrations of tetra- and penta-chlorinated congeners associated with urban and port activities near Paranaguá city. The differences in concentrations between the three sediment cores were attributed to the distance of the sampling points in relation to the possible sources of pollution, which are mostly related to Paranaguá city. The vertical distribution of PCBs in the sediment core P2 was related to historical anthropogenic activities. The highest PCB input was from 1970 to the early 1990s, which coincides with a period of greater use of PCBs in Brazil as well as their greater worldwide production.