The conformational equilibria of the low energy conformers of the repeating units of agarose, i.e. neoagarobiose and agarobiose have been studied theoretically in five solvents. The structure of each individual conformer has been refined by molecular mechanics calculations, from the distinct low-energy regions determined from potential energy surfaces. The stability of the conformers in dilute solution has been evaluated through consideration of the relaxed intramolecular energy including electrostatic, dispersion and cavity terms. For each disaccharide, the calculated abundance of conformers is practically independent of the solvent. Dipole moments and linkage rotation have been calculated for each of the low energy conformers. The calculated molar fractions of the stable conformers were used to model the optical rotation values measured for a single strand of agarose chain in its disordered state, and a satisfactory agreement has been reached (lambda cal = -133 degrees, lambda obs = -145 degrees). For the agarose molecule in the solid state, a left-handed threefold single helix, repeating in 2.85 nm is predicted. Such a helix, which represents the calculated stable conformation for a single strand of agarose, should be considered in descriptions of the molecular basis of sol-gel transition of agarose.