A concise and efficient synthesis of a series of amino-substituted benzimidazole–pyrimidine hybrids has been developed, starting from the readily available N 4 -(2-aminophenyl)-6-methoxy-5-nitrosopyrimidine-2,4-diamine. In each of N 5 -benzyl-6-methoxy-4-(2-phenyl-1 H -benzo[ d ]imidazol-1-yl)pyrimidine-2,5-diamine, C 25 H 22 N 6 O, (I), 6-methoxy- N 5 -(4-methoxybenzyl)-4-[2-(4-methoxyphenyl)-1 H -benzo[ d ]imidazol-1-yl]pyrimidine-2,5-diamine, C 27 H 26 N 6 O 3 , (III), 6-methoxy- N 5 -(4-nitrobenzyl)-4-[2-(4-nitrophenyl)-1 H -benzo[ d ]imidazol-1-yl]pyrimidine-2,5-diamine, C 25 H 20 N 8 O 5 , (IV), the molecules are linked into three-dimensional framework structures, using different combinations of N—H...N, N—H...O, C—H...O, C—H...N and C—H...π hydrogen bonds in each case. Oxidative cleavage of 6-methoxy- N 5 -(4-methylbenzyl)-4-[2-(4-methylphenyl)-1 H -benzo[ d ]imidazol-1-yl]pyrimidine-2,5-diamine, (II), with diiodine gave 6-methoxy-4-[2-(4-methylphenyl)-1 H -benzo[ d ]imidazol-1-yl]pyrimidine-2,5-diamine, which crystallized as a monohydrate, C 19 H 18 N 6 O·H 2 O, (V), and reaction of (V) with trifluoroacetic acid gave two isomeric products, namely N -{5-amino-6-methoxy-6-[2-(4-methylphenyl)-1 H -benzo[ d ]imidazol-1-yl]pyrimidin-2-yl}-2,2,2-trifluoroacetamide, which crystallized as an ethyl acetate monosolvate, C 21 H 17 F 3 N 6 O 2 ·C 4 H 8 O 2 , (VI), and N -{2-amino-6-methoxy-4-[2-(4-methylphenyl)-1 H -benzo[ d ]imidazol-1-yl]pyrimidin-5-yl}-2,2,2-trifluoroacetamide, which crystallized as a methanol monosolvate, C 21 H 17 F 3 N 6 O 2 ·CH 4 O, (VII a ). For each of (V), (VI) and (VII a ), the supramolecular assembly is two-dimensional, based on different combinations of O—H...N, N—H...O, N—H...N, C—H...O and C—H...π hydrogen bonds in each case. Comparisons are made with some related structures.