In the present article, the antimicrobial properties of ethyl 4-amino-2-mercapto-6-arylpyrimidine-5-carboxylate (2a-h) and ethyl 2-(2,4-dinitrophenylthio)-4-amino-6-arylpyrimidine-5-carboxylate (3a-h) were studied. Biginelli typed three component reaction between an aldehyde, ethyl cyanoacetate and a thiourea constituent which gives a rapid facile 3,4-dihydropyrimidine ring (1a-h), which on aromatization using SeO2 and followed by reaction with 1-chloro-2,4- dinitrobenzene giving final product (3a-h). The structures of all synthesized compounds have been established by extensive IR, NMR and Mass studies and were assayed for their antibacterial activity against S. aureus MTCC-96 and E. coli MTCC-443 and antifungal activity against A. niger MTCC-282 and C. albicans MTCC-227 at different concentrations compared with Ampicillin, Chloramphenicol, Ciprofloxacin and Griseofulvin as standard drugs. The activity was measured in the zone of inhibition. Among the all synthesized compounds, 2a, 2d, 3a, 3d and 3g are significantly active against bacterial strain, while other compounds are weakly active. All the compounds are moderate to low active against fungal strain.