Analytical strategies for screening, quantitation and confirmation of a group of 100 pesticides in fruit and vegetable samples by LC-MS and LC-MS/MS were developed. The pesticides studied belong to different chemical families of herbicides, insecticides and fungicides. A selection of some degradation products was also included. Chromatographic separation was performed using a Zorbax Eclipse XDB-C8 column (150 mm × 4.6 mm and 5 µm particle size), and gradient elution with acetonitrile-water (both with 0.1% formic acid) as mobile phase. LC-MS/MS using highly-selective selected reaction monitoring (H-SRM) acquisition mode monitoring two transitions for each compound showed to be the most sensitive methodology. Quantitation was carried out using matrix-matched standard calibration and good linearity of response was demonstrated (r > 0.998). Limits of detection (by acquiring two transitions and with the ion-ratio requirements) ranged between 0.01 and 20 µg/kg were obtained. So, in general, the sensitivity achieved meets the maximum residue levels (MRLs) established by the European Union regulation for food monitoring programs. Pesticide confirmation was carried out following European Union guidelines. In order to prevent false-positives, further confirmatory strategies were proposed. LC-MS in highly-selective selected ion monitoring (H-SIM) mode with accurate mass measurement was used to obtain an orthogonal criterion (exact mass) for confirmation. Accurate mass measurements were always bellow 0.9 mDa for almost all pesticides studied (similar to those described with TOF instruments). A user reversed energy ramp (RER) product ion scan spectra library was generated by means of a data dependent analysis for routine library searching of pesticides. The combination of LC-MS/MS in H-SRM mode and the generation of the RER product ion scan spectra and library search were then used to achieve further confirmation on pesticide analysis. The LC-MS and LC-MS/MS strategies developed were successfully applied for the analysis and confirmation of pesticides in different types of fruit and vegetables samples, and examples of the screening, quantitation and confirmation of pesticides in these samples are shown in this work.