Abstract: A end-column amperometric detection method with capillary electrophoresis for determination of 2-amino-6-mercaptopurine and 8-azaguanine has been established. A 50 cm length of 25 μm i. d., 360 o.d. μm uncoated fused-silica capillary was used. The detection conditions were optimized and the electrochemical behavior was observed. Under the optimal conditions: detection potential of 1.050 V (vs. Ag/AgCl), operating voltage of 21 kV, sample injection of 10 s at 21 kV and 20 mmol/L phosphate solution at pH 7.0 as buffer, the detection limits were 3.0×10^-7 and 2.0×10^-7 mol/L, and the calibration curve showed good linearity with r=0.9992 and r=0.9990 for 2-amino-6-mercaptopurine and 8-azaguanine, respectively. The daytime RSD of reproducibility for peak current was 2.44% and 3.46%, respectively. The method was successfully applied to determine serum samples. The recovery was found in the rang of 100%～113％ for 2-amino-6-mercaptopurine and 93.0%～102％ for 8-azaguanine, respectively.