The propensity of hydrogen-bonded guanidinium (G) organodisulfonates (S) to form crystalline inclusion compounds has been investigated in the context of separating isomeric mixtures of xylenes and dimethylnaphthalenes via selective inclusion. Pairwise competition experiments, in which inclusion compounds are grown from solutions containing an isomeric mixture of guests, map the inclusion selectivity of a particular host as a function of guest content in solution. Whereas the G(2)[4,4 ' -biphenyldisulfonate] host is minimally selective with respect to inclusion of o-, m-, or p-xylene, the homologous G(2)[2,6-naphthalenedisulfonatel is highly selective toward the inclusion of p-xylene, by a factor of 36 and 160 versus o-xylene and m-xylene, respectively. Similarly, the hosts of the homologous series G2[2,6-naphthalenedisulfonatel, G(2)[4,4 ' -biphenyldisulfonate], G(2)[2,6-anthracenedisulfonatel, and G(2)[4,4 ' -azobenzenedisulfonatel display different selectivity for the 10 isomers of dimethylnaphthalene. The details of the selectivity behavior are highly dependent on the molecular structure of the GS host and the solid-state structures of the corresponding inclusion compounds. Single crystal structure determinations reveal that isomer selectivity is most pronounced when the structures of corresponding inclusion compounds are significantly different, i.e., when the isomeric guests template different architectural isomers of the host. Furthermore, selectivity appears to be a consequence of size and shape compatibility between the host and guest. The observation of selective inclusion demonstrates the feasibility of a crystallization-based separation process based on these host compounds.