A computational study of the relative stability of the monolacunary Keggin polyoxotungstates alpha and beta(3)-[XW11O39](m-) (X = P, m = 7; X = Si, m = 8) was performed. The influence of the nature of different grafted cations and of the central anion XO4n- on the relative stabilities of the lacunary isomers was analyzed. From these results, an interpretation of the structural difference in the metallic frameworks of alpha-[PW11O39{Ru(DMSO)(3)(H2O)}](5-), alpha-[PW11O3{Ru(C6H6)(H2O)}](5-), and beta(3)-[SiW11O39{Ru(DMSO)(3)(H2O)}](6-) is proposed, and conclusions are drawn as to how to favor the formation of beta(3) derivatives in future syntheses.