Flowing afterglow atmospheric pressure glow discharge tandem mass spectrometry (APGD-MS/MS) is used for the analysis of trace amounts of pesticides in fruit juices and on fruit peel. The APGD source was rebuilt after Andrade et al. (Andrade et al., Anal. Chem. 2008; 80: 2646-2653; 2654-2663) and mounted onto a hybrid quadrupole time-of-flight mass spectrometer. Apple, cranberry, grape and orange juices as well as fruit peel and salad leafs were spiked with aqueous solutions containing trace amounts of the pesticides alachlor, atrazine, carbendazim, carbofuran, dinoseb, isoproturon, metolachlor, metolcarb, propoxur and simazine. Best limits of determination (LODs) of pesticides in the fruit juices were achieved for metolcarb (1 μg/L in apple juice), carbofuran and dinoseb (2 μg/L in apple juice); for the analysis of apple skin best LODs were 10 pg/cm2 of atrazine, metolcarb and propoxur which corresponds to an estimated concentration of 0.01 μg/kg apple, taking into account the surface area and the weight of the apple. The measured LODs were within or below the allowed maximum residue levels (MRLs) decreed by the European Union (1-500 μg/kg for pesticides in fruit juice and 0.01-5 μg/kg for apple skin). No sample pretreatment (extraction, pre-concentration, chromatographic separation) was necessary to analyze these pesticides by direct desorption/ionization using APGD-MS and to identify them using MS/MS. This makes APGD-MS a powerful high-throughput tool for the investigation of very low amounts of pesticides in fruit juices and on fruit peel/vegetable skin.