An aqueous capillary electrophoretic method was developed for chiral analysis of the novel anti-diabetic drug, sitagliptin. The acid-base profiling of the analyte was carried out using both capillary electrophoresis and nuclear magnetic resonance pH titrations. The apparent complex stability and chiral separation properties were investigated with 30 different cyclodextrins under acidic conditions. The effect of concentration and pH of the BGE, temperature of the capillary, and the type and concentration of the chiral selector on the enantiomer resolution were thoroughly investigated. The effects of dual cyclodextrin systems on separation were also extensively studied. Complete separation of racemic sitagliptin with good resolution (R-S = 2.24) was achieved within a short time (15 min) with optimized parameters (10 degrees C, pH = 4.4, 40mM phosphate buffer) of a sulfobutylether-beta-cyclodextrin (averaged degree of substitution similar to 4) and native beta-cyclodextrin dual system. The averaged stoichiometry of the inclusion complex was determined using the Job plot method with both H-1 and F-19 NMR experiments and resulted in a 1:1 complex. The structure of the inclusion complex was elucidated using 2-D ROESY NMR experiments.