A high-performance liquid chromatographic method, with electrospray ionisation tandem mass spectrometry (HPLC-ESI-MS-MS) for detection, has been developed for the determination of thiabendazole, carbendazime, and phenylurea pesticides in fruit matrices. During the validation process the method was tested for matrix effects, blanks, and the stability of the system. Considerable unspecific matrix effects in the ESI (+) process were detected by comparing standard calibration, and matrix calibration, although blank values were very low and the specific calibration functions showed only small standard deviations. This effect was overcome by using a more complex clean-up, i.e. an additional size-exclusion step.