Medicinal plants have recently gained increasing scientific interest as an important source of molecules with different therapeutic potentials. Accordingly, the present study was carried out to investigate ultrastructural changes induced by the aqueous extract of Solanum incanum (SI) fruit on human colorectal carcinoma cell line (HCT 116 cells). Examination of SI-treated HCT 116 cells with transmission electron microscopy (TEM) demonstrated numerous ultrastructural changes in the form of loss of the surface microvilli, mitochondrial damage and dilatation of cristae, and formation of autophagic vacuoles and increasing numbers of lipid droplets. Also, majority of the treated cells showed nuclear shrinkage with chromatin condensation and nucleolar changes. Moreover, some cells showed focal areas of cytoplasmic degeneration associating with formation of myelin figures and fatty globules. In conclusion, TEM was able to verify cytotoxicity of SI aqueous extract against HCT 116 colon cancer cells.