Reactions in water as a safe and cheap solvent is a major goal of green chemistry. Actual synthesis of pyrido-dipyrimidine scaffold, named DNA-base hybrids, involves catalysis in hazardous solvents. Here we synthesised pyrido-dipyrimidines by one-pot heterocyclization of thiobarbituric acid, vanillic aldehydes and amines in water. Enamine and vanillidene are key intermediates of the Biginelli-like reaction mechanism. Our synthetic method displays several benefits such as the use of a green medium and various substrates, and yields up to 99%.