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In the title compound, 2,4-di­amino-5-(3,4,5-tri­methoxy­benzyl)­pyrimidinium hydrogen malonate, C14H19N4O3+·C3H3O4−, the trimethoprim mol­ecule is protonated at one of the pyrimidine N atoms. The carboxyl­ate group of the hydrogen malonate ion accepts a pair of N—H⋯O hydrogen bonds from an adjacent trimethoprim mol­ecule, which is similar to the carboxyl­ate–trimethoprim cation interaction present in the complex of di­hydro­folate reductase with trimethoprim. An O atom of the carboxyl group forms an intramolecular O—H⋯O hydrogen bond with the carboxyl­ate group, leading to a folded conformation for the hydrogen malonate ion. Each hydrogen malonate ion bridges two di­amino­pyrimidine cations, via N—H⋯O and C—H⋯N hydrogen bonds, leading to a supramolecular ribbon made up of alternating cations and anions. Two such inversion-related ribbons are cross-linked by (amino)N—H⋯O(methoxy) hydrogen bonds, (pyrimidine)C—H⋯O(methoxy) hydrogen bonds and π–π stacking involving the benzene planes. [ABSTRACT FROM AUTHOR]