Direct separation has been achieved between two isomers, which are conforming to each other. A conformeric mixture of C3V and CS conformers of RDX and α‐ and β‐conformers of HMX have been separated by High Performance Liquid Chromatography (HPLC) using a Nova‐Pak RC18 column and MeOH‐H2O mixtures (50 : 50 to 20 : 80) as mobile phase. The absolute configuration of each separated conformer has been investigated on the basis of the reported heat of formation and dipole moment.