The objective of this study was to investigate whether there were any differences in the heavy metals and nitrate contents in organic and conventional tomatoes (Robin-F1, Amati-F1, and Elpida-F1). The tomato as a fruit vegetable is not characterized by high accumulation of heavy metals and nitrates. We found significantly greater concentrations of Pb, Zn, Cu, and Ni in conventional tomatoes, but we found the growing method to have no influence on cadmium Cd, Co, and Cr levels in all cultivars. In the present study, the detected levels of contaminants were found to be markedly lower than the maximum limits allowed by law. The concentrations of heavy metals in tomato fruit decreased in the order Zn>Pb>Cu>Cr>Ni>Co>Cd. This study confirms that the most important variable in the nitrate content of tomatoes is cultivar. The lowest content of nitrates is registered in the variety Elpida, especially in the organically fertilized (20 mg·kg^-1). The nitrate content in this study is presented as the average of all cultivars, and it was found to be lower in organic production (29%-41%) compared to conventional production systems.