The molecular structure, stabilization energy, and thermodynamic properties of the plausible modes of the interaction for the three possible alpha-cyclodextrin (alpha-CD) dimers (head-to-head, tail-to-tail, and head-to-tail) with a water cluster were obtained using quantum chemical methods for the first time. Nine distinct spatial arrangements were investigated. The head-to-head mode of interaction with water is preferred by more than 10 kcal.mol(-1) (BLYP/6-31G(d,p)//PM3 Gibbs free energy difference value at room temperature) in relation to the next stable structure, with a water dimer structure placed inside each cavity and cyclic water tetramers surrounding each tail end. The inter alpha-CD hydrogen bonds play a major role to stabilize the dimeric structures, with no water tetramer being found between the two alpha-CD subunits for the preferred global minimum structure. Therefore, a theoretical model aimed to describe the behavior of alpha-CD dimer, or their inclusion complexes, in the aqueous media should take into account this preference for binding of the water molecules.