Plants are often exposed to external biotic or abiotic agents that can damage cells. Biotic agents include molecules produced by pathogens, and abiotic agents include ultraviolet radiation, heavy metals and xenobiotic agents such as herbicides. Because of the importance of abiotic stresses and the limited knowledge of the defense responses of plants to stresses, a study was conducted using flow cytometry to evaluate endocellular events in protoplasts of two tomato species, Lycopersicon hirsutum and Lycopersicon esculentum, following exposure to 10 mM CuCl2 and 1% paraquat. During the first 30 min of exposure to 10 mM CuCl2, mean fluorescence intensity values in both species decreased by more than 50% compared to the untreated control. During the first 30 min of paraquat treatment, the production of reactive oxygen species, evaluated as the incidence of protoplasts in which the superoxide anion was present, was 32.9 % and 25.4%, respectively, for L. hirsutum and L. esculentum. Hyperpolarization of the mitochondria for both tomatoes species was observed during the first 2 h. The absence of early membrane damage and the markedly detrimental effects of the treatments on the mitochondria suggest that additional mechanisms which lead to cell death may be involved in these processes, and that these mechanisms may be associated with apoptosis.