In this study, the stabilities of trans-2,3- and trans-2,5-dihalo-1,4-dioxanes conformers were investigated at the LC-BLYP/6-311+G(d,p) theory level. The total energies and dipole moments of the axial and equatorial conformations were calculated for the mentioned molecules. The stability of theconformers, bond distances and spin-spin coupling constants of C-Hax and C-Heq bonds were explained with the negative hyperconjugative anomeric effects. The negative hyperconjugative anomeric effects on these conformers were illustrated using the natural bond orbital (NBO) analysis. Deformation maps of electron density for these conformers were provided, as well. In the basis of these calculations, the axial conformer was more stable than equatorial conformer in the studied molecules. Moreover, the trans-2,3- and trans-2,5-dihalo-1,4-dioxanes molecules were iso-energetic.