The study of pesticide residues belonging to endocrine disrupting chemicals (EDCs) (23 analytes of different chemical classes--organochlorines, organophosphates, pyrethroids, dicarboximides, phtalamides, dinitroanilines, pyrazole, triazinone) in apple matrix with conventional capillary GC-NCI-MS (with methane as reagent gas) in comparison to EI ionization is presented. For sample preparation QuEChERS method was applied. The lowest calibration levels (LCLs) for all pesticides were determined in both modes. Calibration in the NCI mode was performed at the concentration levels from 0.1 to 500 microg kg(-1) (R(2) > 0.999) and for EI in the range from 5 to 500 microg kg(-1) (R(2) > 0.99). From LCLs the instrumental limits of detection (LODs) and quantification (LOQs) were calculated. Chemometric study of pesticide signals in two MS modes was performed. Repeatability of all measurements, expressed by the relative standard deviations of absolute peak areas was better than 10% for the majority of compounds. Significantly lower values were obtained for the NCI mode.