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The asymmetric unit of the title compound, C4H12N22+·2ClO4−·2H2O, contains half of a piperazinediium cation, one perchlorate anion and one water molecule. The diprotonated piperazine ring, which is completed by crystallographic inversion symmetry, adopts a chair conformation. In the crystal structure, the cations and anions are linked by intermolecular N—H...O and O—H...O hydrogen bonds into a three-dimensional network.