This paper describes the enhanced separation of adenine (A), hypoxanthine (HX), 8-azaadenine (8-AA), thymine M, cytosine (C), uracil (U) and guanine (G) by CZE dispersing carboxylic multiwalled carbon nanotubes (c-MWNTs) into the running buffer. The effect of important factors such as c-MWNT nanoparticle concentration, the acidity and concentration of running buffer, and separation voltage were investigated to acquire the optimum conditions. The seven purine and pyrimidine bases could be well separated within 16 min in a 35cm effective length fused-silica capillary at a separation voltage of +8.0 kV in a 23 mM tetraborate buffer (pH9.2) containing 8.0 x 10(-5) g/mL c-MWNTs. Under the optimal conditions, the linear ranges were of 2-250 mu g/mL for A (R-2 = 0.995), 3-200 mu g/mL for U (R-2 = 0.990) and G (R-2 = 0.992), 3-250 mu g/mL for T (R-2 = 0.998), 2-200 mu g/mL for C (R-2 = 0.985) and 4-200 mu g/ml for HX (R-2 = 0.988) and 8-AA (R-2 = 0.990). The detection limits were 0.9 mu g/mL for A (S/N = 3), 2.4 mu g/mL for U, 2.0 mu g/mL for T, 1.5 mu g/mL for C, 2.5 mu g/mL for G and 3.0 mu g/mL for HX and 8-AA. The proposed method was successfully applied for determining five purine and pyrimidine bases in yeast RNA.