In the scope of this study, pesticide residue distribution within a fruit and the possible error deriving from sample preparation step were demonstrated with the analysis of benomyl residues in peel, pulp, and seeds of papaya fruits treated post-harvest. Benomyl residue, measured as carbendazim, in corresponding sections of peel and pulp of papaya fruits ranged from 0.178 to 1.325 mg/kg and 0.025 to 0.087 mg/kg, respectively. Residue concentration decreased in a range between 41 and 83 % by peeling of papaya. All seeds contained residue value below limit of quantification. As the residues are unevenly distributed among the peel, pulp, and seed, pesticide residue analysis should be carried out accurately according to proper sample preparation protocol in peel, pulp, or in whole fruit and evaluated correctly taking into consideration the purpose of the analysis. The proportion of peel and pulp after their separation significantly affected the residues measured in the peel and pulp. It shows how peeling operation can affect the results and how important it is to remove the peel without significant portion of pulp attached to it. Thus, the selected test system could be well used to demonstrate the possible variability of measured residues depending on the uniformity of sample preparation.