A series of 6-methyl-4-[1-(2-substituted-phenylamino-acetyl)-1H-indol-3-yl]-2-oxo/thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid ethyl esters (1-16) were synthesized and evaluated in vitro for their antimicrobial and anticancer potential. 6-Methyl-4-{1-[2-(4-nitro-phenylamino)-acetyl]-1H-indol-3-yl}-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid ethyl ester (15, pMIC(ec) = 2.50 μM/mL) was found to be almost equipotent to the standard drug, norfloxacin (pMIC(ec) = 2.61 μM/mL) against Escherichia coli and emerged as most potent antimicrobial agent (pMIC(am) = 1.84 μM/mL). 4-{1-[2-(2-Chloro-4-nitro-phenylamino)-acetyl]-1H-indol-3-yl}-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid ethyl ester (4, IC(50) = 5 μg/mL) was more potent than the standard drug 5-fluorouracil (IC(50) = 6 μg/mL) against HCT-116 a colon cancer cell line, and emerged as the most potent anticancer agent. The QSAR studies demonstrated the importance of topological parameter, Balaban index (J) followed by lipophillic parameter, log P in describing the antimicrobial activity of the synthesized compounds.