The separation and migration behavior of seven positional and structural neutral alkylnaphthalene derivatives in cyclodextrin-mediated capillary electrophoresis were systematically investigated. The effective separation conditions were to use 10mm phosphate buffer with negatively charged carboxymethyl-beta-cycloclextrin (CM-beta-CD) at pH 6.0. The guest-host interactions with 1:1 or both 1:1 and 1:2 binding stoichiometries for various derivatives were evaluated by comparing their apparent binding constants. The results reveal that the substituent group(s) attached to the naphthalene ring significantly affected the inclusion stoichiometric behaviors. Alkylnaphthalene derivatives with the substituent(s) at the 1-position(s), such as 1-ethyl naphthalene, 1,4-di methyl naphthalene, may undergo complexation with one and two CM-beta-CD molecules. The binding constants of these derivatives were consistent with the data obtained by a spectrophotometric method. The thermodynamic parameters were also calculated in order to improve our understanding of the interaction between the neutral alkylnaphthalene derivatives and CM-beta-CD at various temperatures. The positive entropy (AS') values of the alkylnaphthalenes with the substituent(s) at the 2-position(s) indicate that the inclusion of the guest molecule into the cavity of CM-beta-CD is favored at all temperatures.