The crystal structures of two quinoxalinedione derivatives, 6,7-dimethyl-1,4-dihydro-2,3-quinoxalinedione dihydrate (1) and 6,7-dimethoxy-1,4-dihydro-2,3-quinoxalinedione hydrate (2), and AM1 molecular orbital computational investigations of electronic properties and hydrogen bond strengths are reported. The space group for1iswitha = 7.0109(1) Å,b = 8.5901(3) Å,c = 10.7890(5) Å, α = 112.704(3)°, β = 96.053(3)°, and γ = 107.589(2)°. For2, the space group isPbcawitha = 12.2769(6) Å,b = 6.9291(3) Å, andc = 25.8644(7) Å. The geometries of these two compounds are similar; small differences are mostly due to the different electronic characters of the substituents and to intermolecular interactions in the crystals. There are two main factors determining the packing schemes of these compounds, π-stacking between neighboring molecules and hydrogen bonds, including bonds with the water molecules of crystallization. The AM1 semi-empirical calculations show differences between net atomic charges and dipole moments. For both structures, calculations confirm the asymmetry of hydrogen bonds that is observed in the crystal structures.