Solanum chacoense (wild potato) is intensively used in breeding, its biochemical profile and putative human health-related traits being transferred into potato cultivars aimed for consumption. The goal of this study was to evaluate the biochemical profile and the anti-tumor potential of methanolic extracts obtained from S. chacoense leaves and tubers against three breast cancer cell lines in comparison to healthy endothelial cells (HUVEC). The biochemical profile of the extracts was determined by HPLC-PDA/-ESI⁺-MS and ITEX/GC-MS, the selective cytotoxicity by MTT assay whereas RT-qPCR was used to evaluate the expression of proliferation- and apoptosis-related genes. Both extracts proved to be rich in phenolic acids and volatile compounds, the leaf extract also containing glycoalkaloids. Both extracts proved to be cytotoxic for breast cancer cell lines, with IC₅₀ values varying between 132.9 and 390.7 µg/ml. Both extracts had selective cytotoxicity against MCF7 cell line in comparison to HUVECs (selectivity coefficients >2.3). The treatment with the extracts induced overexpression of the pro-apoptotic gene BAX¸ down-regulation of the anti-apoptotic gene BCL-2 and the pro-proliferation genes NFkB, CCND1, and STAT3. Thus S. chacoense extracts proved to be rich in compounds with anticancer proprieties and are capable of inducing selective cytotoxicity on MCF7 cell line.