Gas chromatography (GC) and ion trap mass spectrometry (MS) were combined with microchip atmospheric pressure chemical ionization (microAPCI) and microchip atmospheric pressure photoionization (microAPPI) sources. Selected polychlorinated biphenyls (PCBs, IUPAC Nos. 28, 52, 101, 118, 138, 153 and 180) were analyzed by GC/microAPCI-MS and GC/microAPPI-MS to demonstrate the applicability of the miniaturized ion sources in negative ion mode analysis. The microAPCI and microAPPI methods were evaluated in respect of detection limit, linearity and repeatability. The detection limits for the PCB congeners were somewhat lower with microAPCI than with microAPPI, whereas microAPPI showed slightly wider linear range and better repeatability. With both methods, the best results were obtained for highly chlorinated or non-ortho-chlorinated PCBs, which possess the highest electron affinities. Finally, the suitability of the GC/microAPPI-MS method for the analysis of PCBs in environmental samples was demonstrated by analyzing soil extracts, and by comparing the results with those obtained by gas chromatography with electron capture detection (GC/ECD).