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Chlorothalonil is a non-systemic fungicide that is easily degraded in contact with plants and soil or even by the effect of light and pH. A method for the determination of chlorothalonil in courgettes, strawberries, oranges, leeks and tomato by solvent extraction followed by GC-MS/MS with a triple quadrupole analyser was developed. The causes of chlorothalonil degradation during sample treatment were studied and minimised. The final method was based on extraction with acetone in the presence of 0.1?M EDTA sodium salt solution, and clean-up by SPE using OASIS HLB cartridges. Isotope-labelled hexachlorobenzene (HCB-13C6) was added as an internal standard to the SPE extracts before analysis by GC-MS/MS (EI) (QqQ) analysis in order to correct for instrumental deviations. Quantification was performed by matrix-matched standard calibration using relative responses to the internal standard. Two MS/MS transitions were used for mass spectrometric determination of chlorothalonil to ensure reliable quantification and confirmation. The method was validated using blank samples (for all matrices) spiked at two levels. Recoveries between 77% and 110% and an RSD below 20% were obtained for 0.1 and 0.01?mg?kg-1 spiking levels (n?=?5). The validated method was applied to treated and untreated samples collected from an experimental field where a chlorothalonil formulated was applied.