Charge density distribution analysis supplemented by energy studies of two known (previously reported) polymorphic forms of benzidine dihydrochloride — triclinic P1̅ (TP) and orthorhombic Pbcn (OP) — is presented. High resolution X-ray diffraction measurement results were additionally related to the theoretically evaluated charge density distribution on the basis of periodic ab initio computations. In the case of TP, collected neutron diffraction structural data were included in the high resolution X-ray multipole refinement procedure. Although TP and OP form generally similar layered crystal architectures, the two structures differ significantly in details, due to slightly different conformations of the benzidinium cation, different packing, and thus intermolecular interactions. This is reflected in charge density distribution, crystal morphology, and growth. For TP, the integrated charge for the chloride anions is equal to ca. −0.90e, while for OP it is −1.07e. In consequence, charges for the benzidinium cation are equal to +1.85e for TP and +2.12e for OP. Different charge distributions for both polymorphs cause significant differences in the electrostatic potential. In the case of OP, the electrostatic potential for the −NH3+ group is substantially higher than for TP. Lower values of charge density at aromatic rings of the benzidinium cation for TP can be associated with significant contribution of stacking type of interactions. TP is slightly (ca. 10–15 kJ·mol–1) more thermodynamically advantageous than OP, however, the difference constitutes just a small percentage of the total cohesive energy derived (ca. −1500 kJ·mol–1). Therefore, both polymorphic forms can be obtained simultaneously from one solution under the same conditions. On the other hand, TP is characterized by a more homogeneous distribution of ionic fragments in its crystal lattice than OP. The straightforward comparison of the crucial interlayer interaction energies and the surface free energy values between both polymorphs shows that in the case of TP crystal faces should more preferably grow, being slightly less stable than in OP. Lower surface free energy in OP, and especially low interlayer interaction energy of (100) slabs, presumably hampers further growth of the initially formed crystals, explaining the difficulties in obtaining OP crystals of the size suitable for neutron diffraction experiments. Naturally, kinetic and solvent effects should not be neglected. Nevertheless, the energy results show that despite the resemblance of the cohesive energy values of polymorphs, the character and features of their crystal architectures may cause significant differences in crystallization mechanisms and crystal quality. It appears that there is little correlation between geometrical parameters of hydrogen bonds and their energies.