We developed a new instrumental approach, termed Supersonic GC-MS, which achieves fast, sensitive, confirmatory and quantitative analysis of a broad range of pesticides in complex agricultural matrices. Our Supersonic GC-MS system is a modification of a bench-top Agilent 6890 GC+5972 MSD with a supersonic molecular beam (SMB) interface and fly-through EI ion source. One of the main advantages of Supersonic GC-MS is an enhanced molecular ion (M+) in the resulting mass spectra. For example, the M+ was observed in all 88 pesticides that we studied using the Supersonic GC-MS whereas only 36 of 63 (57%) pesticides that we investigated in standard GC-MS exhibited a M+. We also found that the degree of matrix interference is exponentially reduced with the fragment mass by about 20-fold per 100 amu increasing mass. The enhancement of the M+ combined with the reduction in matrix background noise permit rapid full scan analysis of a potentially unlimited number of pesticides, unlike selected ion monitoring or MS-MS in which specific conditions are required in segments for targeted pesticides. Furthermore, unlike the case with chemical ionization, EI-SMB-MS spectra still give accurate identification of compounds using common mass spectral libraries. In practice,we found thatlibraries favor mass spectra in which the M+ appears, thus Supersonic GC-MS produced better spectra for compound identification than standard GC-MS. To achieve even lower identification limits, the M+ plus a second major ion (still using full scan data) gives higher signal-to-chemical noise ratios than the traditional 3-ion approach. The replacement of two low-mass ions with the M+ (supersonic two-ions method) results in a significant reduction of matrix interference by a factor of up to 90. Another main advantage of Supersonic GC-MS is its exceptional suitability for fast GC-MS with high carrier gas flow-rate. Fast Supersonic GC-MS was able to analyze thermally labile pesticides, such as carbamates, that are difficult or impossible to analyze in standard GC-MS. Large volume injection using a ChromatoProbe was also demonstrated, in the 6 min analysis of pesticides at 20 ng/g in a spice matrix.