Abstract In the present work a novel series of indol-5,8-pyrimido[4,5-d]pyrimidine derivatives (4a-l) have been synthesized by Biginelli reaction of barbituric/thiobarbituric acid, substituted indole-3-carboxaldehyde and substituted aryl amines in aqueous ethanol using 10 mol% CAN as a catalyst. The synthesized compounds (4a-l) were evaluated for in vitro antibacterial and anticancer activities. In addition to this, in silico molecular docking studies was also performed to predict the binding interactions of synthetic molecules with appropriate target molecules in connection to their antimicrobial and anti-cancer effects. Among the compounds tested, compounds 4d, 4 g and 4 h were found to have effective antibacterial activity against the tested pathogens. The cytotoxicity studies of synthesized pyrimidine derivatives were found to be effective against K-562, HeLa, MCF-7 and Hepg-2 cancer cell lines.