A simple and efficient approach towards single step synthesis of 6-amino-5-cyano-2-(hydroxy/mercapto)-4- substitutedpyrimidine derivatives has been developed by three component condensation of aromatic aldehydes, malononitrile and urea or thiourea using conventional heating and microwave irradiation technique. Some of these novel derivatives showed moderate to potent in-vitro antibacterial, antifungal and antitubercular activity.