Occupying a prominent place in the human diet, being widely marketed and consumed in the world, the tomato (Lycopersicon esculentum Mill) stands out for being a food rich in vitamins, mineral salts and antioxidant components such as carotenoids and flavonoids. In this way, a study was started on the effects of the use of agrochemicals in the tomato crop. Initially, hexanic and ethanolic extracts were obtained from both organic and conventional tomatoes, then a comparative thin layer chromatography of the extracts was carried out using as mobile phase a mixture of hexane and acetone in different proportions. The extracts were then fractionated by column chromatography (CC), at first was used as the mobile phase only hexane, then a mixture of hexane and acetone, after, only acetone and finally ethanol, subsequently these fractions were evaluated by gas chromatography coupled to mass spectrometry. In the hexanic subfractions that were derivatized with the BSTFA it was possible to observe that the hexanic subfraction of organic tomato presented two peaks in 9.3 min and 10.8 min, but did not appear in the hexanic subfraction of conventional tomato. Thus, showing an influence of agrochemicals on natural chemical constituents when used in tomato crops. Already in the chromatograms of the subfractions, after derivatization of carboxyl, it was observed peaks of greater intensities in 4.9 min and 5.7 min, when these were evaluated in the library of the masses, they suggested to be compounds derived from oxalic acid and heptadecane.