The interactions of two medicines of rutin and chloramphenicol with beta-cyclodextrin were investigated using mobility shift method by capillary electrophoresis. The size of the capillary column was 37 cm x 50 microm i.d. with an effective length of 30 cm. The running buffer was a mixture of 25 mmol/L sodium borate and 100 mmol/L boric acid (pH 8.6). Effective mobilities of the two medicines changed with altering the concentration of beta-cyclodextrin. By nonlinear least square fitting curve, the inclusion constants of 98.5 and 1 204 L/mol for rutin and chloramphenicol were obtained at 25 degrees C, respectively. The inclusion constants at different temperatures were determined, from which a series of thermodynamic parameters were derived. Experimental results show that an obvious relationship of mutual compensation between enthalpy and entropy existed in these inclusion reactions. The most stable configurations of the inclusions were calculated using MM2 force field, and the results were well in agreement with the experimental results.