An efficient and direct procedure for the synthesis of pyrimido[4,5-d] pyrimidine derivatives from three component condensation of an aromatic aldehyde, urea/ thiourea and barbituric acid was carried out by using aqueous tetrabutyl ammonium bromide (TBAB) under solvent-free microwave conditions, which devoids hazards of solution phase reactions. The reaction time has been brought down from minutes to seconds with improved yield as compared to reported method.