An optimized method using stir bar sorptive extraction (SBSE) for the determination of 25 polychlorinated biphenyls (PCBs) from water samples among them three of the most toxic coplanar PCBs (PCB 77, PCB 126 and PCB 169) was developed. Since the investigated PCBs comprise all steps of chlorination (from PCB 1 as monochlorobiphenyl to PCB 209 as decachlorobiphenyl) the results should be representative for the total class of the 209 PCB congeners. For 8 ml spiked water samples with 2 ml methanol addition and 2 h exposure time of stir bars recoveries between 28% (PCB 209) and 93% (PCB 1, PCB 52, PCB 77) were found. Detection limits between 0.05 ng/l and 0.15 ng/l were calculated for the combination of SBSE and thermodesorption-GC/MS. The procedure was applied to the investigation of groundwater and river water samples from the industrial region of Bitterfeld northern Leipzig, Germany.