Gas or liquid chromatography coupled with mass spectrometry is among the most reliable analytical techniques used in pesticide residue analysis. The existing problem in pesticide analysis in complex matrices such as fruit is the variation in analyte chromatographic response caused by matrix components, which is called the matrix effect. These effects can be evaluated quantitatively by comparing the response of equal analyte concentrations in a solvent and in the post extraction fortified sample extract. The response of the 5 µg mL-1 solution of fungicides pyrimethanil, cyprodinil, from the class of anilinopyrimidines and trifloxystrobin from the class of strobilurins, commonly used in the protection of apple crops, was evaluated in pure hexane and in different concentrations of peel and flesh hexane extracts of Granny Smith apple variety. The response of trifloxystrobin was not significantly changed in either of two matrices, while a significantly more different response of pyrimethanil and cyprodinil was observed in both peel and flesh extracts than in the pure solvent. In the undiluted flesh extract, the matrix effect reached 154% and 76% for pyrimethanil and cyprodinil, respectively. In the undiluted peel extract, the values were-49% for pyrimethanil and-30.2% for cyprodinil. The response variation of these pesticides remained high, even after the matrix dilution. The final matrix dilution resulted in about 2-times lower response variation for both pesticides in flesh extract-based standards, while in peel extract-based standards the manifestation of inversion was observed.