This paper describes method validation for determination of more than 40 pesticides in apples using a GC technique. Target compounds belonged to the organochlorine, organophosphorus, carbamates, pyrethroids, triazoles, dicarboximides and strobilurins groups, among others. Sample preparation consisted of acetone extraction and subsequent cleanup/concentration by SPE with a polymer-based sorbent. Single quadrupole GC-MS operating in SIM mode and electron impact ionization was used for identification and quantification of the pesticides. Average recoveries for analytes ranged between 70 and 110% at three fortification levels - 0.01, 0.1 and 0.2 mg kg(-1). Relative standard deviations were lower than 20% for all tested compounds. Calculated limits of detection and limits of quantification were below 0.01 mg kg(-1), which were sufficiently low compared to the maximum residue levels (MRLs) established by European legislation. The proposed method was applied for determination of pesticide residue in four selected apple varieties after harvesting. Whole and processed fruits (peel and peeled fruits) were analyzed from different treatment systems: two conventional, one based on integrated pest management (IPM) and two variants based on organic production (controls). Higher levels of pesticide residues were found in apple fruits under conventional conditions. Fenitrothion and chlorpyrifos residues were detected frequently in apple peel at concentrations up to 0.45 and 0.77 mg kg(-1), respectively. The levels found in the whole fruits of the same samples were much lower than in peel and below the respective MRLs (0.5 mg kg(-1) for both pesticides). Measurable residues of triadimenol only, up to 0.05 mg kg(-1), concentrated in the peel, were found in the apples from IPM.