Capillary electrophoresis was applied to separate purine and pyrimidine bases in the basis of their partial ionization in the alkaline buffer. The effects of buffer pH, buffer and beta-cylclodextrin concentration were systematically investigated using a commercial capillary electrophoresis instrument with UV detector at 254nm. We found that the resolutions of bases (especially for adenine and thymine) were significantly improved in the presence of beta-cylclodextrin. The satisfactory separation of five bases such as cytosine, thymine, adenine, guanine and uracil were achieved by capillary electrophoresis using beta-cylclodextrin as an additive. Under the optimal conditions, the linear range was from 2 to 200microg/ml for bases (R= 0,991-0,9977 ) and the detection limits were from 0.8 to 1.8microg/ml (S/N = 2). The detection limit of 0.05microg/ml ( S/N=2 ) for uracil was obtained by stacking injection mode. The assay was used to determine the deamination of cytosine to uracil by heating in the presence of sodium hydroxide. Our primarily results show that capillary electrophoresis is a very useful tool for determination of purine and pyrimidine bases and study on nucleic acids.