Benzimidazoles of both natural and synthetic sources are the key components of many bioactive compounds. Several reports have shown antifungal, antiviral, H2 receptor blocker and antitumor activities for benzimidazoles and their derivatives. In-vitro cell-based cytotoxicity assay is an easy and cost effective tool for hit ranking and lead optimization at the early stage of drug discovery. In the present study, novel bis-benzimidazole derivatives were screened for cytotoxicity against HEK-293T (Human erythrocyte kidney cell line), MDA-MB453 (Human Breast carcinoma cell line), MDA-MB468 (Human Breast carcinoma cell line), NCI-H522 (Human Lung cancer cell line) and NCI-H23 (Human Lung cancer cell line) with use of short term cytotoxicity MTT assay protocol. Compound 9c, 9g, 9i have exhibited significant cytotoxic activity after 48 hrs comparable with standard drug doxorubicin and were considered to be the best candidate of the series that could be a good starting point to develop new lead compounds in the fight against cancer.