In search of new selective anti-cancer agents, a series of sixteen novel 2-aminoimidazole-quinoline hybrid compounds (5a-5p) have been designed and synthesized regioselectively. We have characterized the compounds extensively using IR, 1D and 2D NMR Spectroscopy and mass spectrometry. The cytotoxicity studies against different cancer cell lines showed that the compound 5a (Imd-Ph) emerged as a potent cytotoxic scaffold. Imd-Ph (5a) exhibited a selective anticancer activity against human colon cancer cell line (HCT-116, DLD-1) and was found relatively non-toxic to breast cancer cells (MDA-MB-231) as well as to normal primary endothelial cells (HUVEC). Structure-activity relationship of imidazole-quinoline hybrid scaffolds revealed differential and selective toxicities exerted by the different derivatives against cancer and normal cells. Structural modification of the scaffold with library of a wide variety of substituents may lead to the development of novel selective anti-cancer agents in the future.