The tomato-processing industry, due to the large amount of waste it generates, represents an environmental problem. The medicinal uses of non-edible parts of tomato could reduce biomass accumulation, representing a strategy to avoid environmental impact. By Bligh and Dyer method, we obtained lipid extracts from leaves and seeds of Tomato. The effects of these extracts on C2C12 cell viability were determined using methylene blue assay. Also, we assessed cellular morphology using MitoTracker Red and DAPI dyes. We confirmed apoptosis by terminal deoxynucleotidyl transferase (TdT) dUTP Nick-End Labeling (TUNEL) assay. Using cytometry and Westernblot analysis we found that the extracts induce apoptosis through caspase-3/7 activation. Also, the extracts trigger a defense response through Akt and HSP27.We found that p38 MAPK is responsible for HSP27 phosphorylation. Using real-time polymerase chain reaction, we show that the tomato extracts are able to modulate apoptotic genes; the mRNA levels of p53 upregulated modulator of apoptosis (PUMA) were increased, but of Bcl-2 were down regulated. These results suggest that the tomato extracts could act as apoptotic inducers, useful in medicine. This is the first report on the potential uses, showing molecular concepts, of non-edible parts of Tomato.