Background: Dihydropyrimidinone is considered as a pharmacophoric skeleton in many drug discovery programmes. To explore the activity of dihydropyrimidines, we regioselectively synthesized some of the substituted mannich bases of dihydropyrimidinone (DHPM) analogues regioselectively with fluoroquinolones (Ciprofloxacin). Methods: Regioselectivity in these structures is achieved by the influence of weak base like potassium carbonate and synthesized some novel dihydropyrimidine N- and O-Mannich bases of ciprofloxacin (3a-j, 4a-g) using microwave technology. All the synthesized molecules have been evaluated for their antiviral activity against hepatitis C, hepatitis B, vaccinia, cowpox, severe acute respiratory syndrome, West Nile, dengue, Venezuelan equine encephalitis viruses, Flu A (H1N1, H3N2 and H5N1) and Flu B viral strains as well as for their cytotoxicity using standard protocols. Results: An attempt was made to interpret the structure activity relation of compounds with their antiviral activity data. Compounds 3a, 3e, 3f, 4e, 4g were found to be active against Flu A (H1N1), TCRV, hepatitis B, yellow fever, vaccinia virus respectively. Conclusion: Some of the synthesized compounds exhibited potent activity against some viral strains. Out of O- and N-mannich bases, O-mannich bases were found to be more potent with high selectivity index.