The determination of the relative methylation in DNA tumor samples, in order to evaluate the activity of some anti-cancer drugs, has become a very important issue in the clinical field. Capillary electrophoresis (CE) applications in this area have been done previously but no good separation for model samples or tumor samples has been reported. In this work, the CE conditions have been optimized in order to obtain baseline separation and efficient peaks for cytosine and 5-methylcytosine in both, standard mixtures and actual tumor samples; other bases (adenine, uracil, guanine, and thymine) have also been integrated in the optimization studies. More efficient peaks and shorter analysis time compared with the already reported conditions have been obtained employing a fused-silica capillary (75 microm inner diameter) of 44.5 cm effective length, 20 mM carbonate buffer (pH 9.6) plus 80 mM sodium dodecyl sulfate, a separation voltage of 20 kV, and detection at 223 nm.