This study presents the atmospheric pressure photoionization (APPI) of high-chlorinated (five or more chlorine atoms) polychlorinated biphenyls (PCBs) using toluene as dopant, after liquid chromatographic separation. Mass spectra of PCB 101, 118, 138, 153, 180, 199, 206 and 209 were recorded by using liquid chromatography-APPI-tandem mass spectrometry (LC-APPI-MS/MS) in negative ion full scan mode. Intense peaks appeared at m/z that correspond to [M - Cl + O](-) ions, where M is the analyte molecule. Furthermore, a detailed strategy, which includes designs of experiments, for the development and optimization of LC-APPI-MS/MS methods is described. Following this strategy, a sensitive and accurate method with low instrumental limits of detection, ranging from 0.29 pg for PCB 209 to 8.3 pg for PCB 101 on column, was developed. For the separation of the analytes, a Waters XSELECT HSS T3 (100 mm × 2.1 mm, 2.5 µm) column was used with methanol/water as elution system. This method was applied for the determination of the above PCBs in water samples (surface water, tap water and treated wastewater). For the extraction of PCBs from water samples, a simple liquid-liquid extraction with dichloromethane was used. Method limits of quantification, ranged from 4.8 ng l(-1), for PCB 199, to 9.4 ng l(-1), for PCB 180, and the recoveries ranged from 73%, for PCB 101, to 96%, for PCB 199. The estimated analytical figures were appropriate for trace analysis of high-chlorinated PCBs in real samples.