Scutellaria lindbergii (Lamiaceae) is Iranian species of Scutellaria. Cytotoxic properties of total methanol extract of S. lindbergii and its fractions were investigated on different cancer cell lines including AGS, HeLa, MCF-7, and PC12. Meanwhile the role of apoptosis was explored in this toxicity. Malignant and non-malignant cells were cultured in DMEM medium and incubated with different concentrations of plant extracts. Cell viability was quantitated by MTT assay. Apoptotic cells were determined using PI staining of DNA fragmentation by flow cytometry (sub-G1 peak). S. lindbergii inhibited the growth of malignant cells in a dose-dependent manner. Among solvent fractions of S. lindbergii, the methylene chloride fraction was found to be more toxic compared to other fractions. S. lindbergii-induced a sub-G1 peak in flow cytometry histogram of treated cells compared to control indicating apoptotic cell death is involved in S. lindbergii-induced toxicity. In conclusion, S. lindbergii exerts cytotoxic effects in different cancer cell lines in which apoptosis plays an important role. Thus S. lindbergii could be considered as a potential chemotherapeutic agent in cancer treatment.