Comprehensive two-dimensional gas chromatography (GCxGC) with nitrogen-phosphorus detection (NPD) has been investigated for the separation and quantitation of fungicides in vegetable samples. The detector gas flows (H-2, N-2 and air) were adjusted to achieve maximum response of signal whilst minimizing peak width. The comparison of different column sets and selection of the temperature program were carried out with a mixture of nine N-containing standard fungicides, eight of which were chlorinated. The results from GCxGC-NPD and GCxGC with micro electron-capture detection (mu ECD) were compared. External calibrations of fungicides were performed over a concentration range from I to 1000 mu g L-1. The peak area calibration curves generally had regression coefficients of R-2 > 0.9980, however for iprodione which was observed to undergo on-column degradation, an R-2 of 0.990 was found. The limit of detection (LOD) and limit of quantitation (LOQ) were less than about 74 and 246 ng L-1, respectively. The intra-day and inter-day RSD values were measured for solutions of concentration 0.100, 0.500 and 1.50 mg L-1. For the 0.500 mg L-1 solution, intra- and inter-day precision of peak area and peak height for most of the pesticides were about 2 and 8 , respectively. Excellent linearity was observed for these standards, from 0.001 to 25.00 mg L-1. The standard mixture peak positions were identified by using GCxGC with quadrupole mass spectrometry (qMS). To illustrate the potential and the versatility of both GCxGC-NPD and GCxGC-mu ECD, the method was applied to determination of fungicides in a vegetable extract. Decomposition of one fungicide standard (iprodione) during chromatography elation was readily observed in the two-dimensional (2D) GCxGC plot as a diagonal ridge response in the 2D chromatogram between the degrading compound and the decomposition product.