Objective To establish a high-throughput and accurate quantitative method by high performance capillary electrophoresis (HPCE) for DNA methylation analysis. Methods NaHCO3 buffer containing sodium dodecyl sulfonate (SDS) was used as the running buffer. The operating voltage, column temperature and injection mode were optimized for baseline separation and quantification of nucleosides. Results 5 deoxynucleosides and 5 nucleosides from RNA interference were totally separated in 10min. The calibration equation for deoxycytidine (dC) was Y = 172540.15X-6.19 with correlation coefficient R of 0.999 and the linear range was from 2 × 10-3 mol/L to 2 × 10-1 mol/L. The calibration equation for 5-methyl deoxycytidine (5 mdC) was Y = 170271.74X-46.19 with correlation coefficient R of 0.995 and the linear range was from 1 × 10-4 mol/L to 2 × 10-2 mol/L. The intra-day relative standard deviation (RSD%) was less than 5% and the inter-day relative standard deviation (RSD%) was less than 9%. The detection limit for dC and 5 mdC were both 1 × 10-5 mol/L. Methylation value was calculated as the ratio of 5mdC to the total dC: [5 mdC] / ([5 mdC] + [dC]) × 100%. The methylation level of calf thymus DNA measured using this method was 6.18%, which was consistent with the value observed on high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) and the value reported before on high performance liquid chromatography-UV detector (HPLC-UV). Conclusion The method this study established is fast, high accuracy, good stability and good sensitivity. It could meet the requirement of determination of trace samples and be used in clinical methylation diagnosis.%目的：建立快速准确的高效毛细管电泳（ HPCE ）定量基因组 DNA 甲基化的方法。方法以含有十二烷基磺酸钠（SDS）的碳酸氢钠溶液作为背景电解质溶液，优化运行电压、柱温，对DNA组成单元脱氧核苷酸进行分离定量。结果5种脱氧核糖核苷和5种核糖核苷在10 min 内实现基线分离。脱氧胞苷（dC）的标准曲线为Y ＝172540.15X-6.19，相关系数（R）为0.999，线性范围从2×10-3 mol／L 到2×10-1 mol／L。5-甲基脱氧胞苷（5 mdC）的标准曲线为 Y ＝170271.74X-46.19，相关系数（R）为0.995，线性范围从1×10-4 mol／L 到2×10-2 mol／L。日内相对标准偏差（RSD％）<5％，日间相对标准偏差（ RSD％）<9％。5 mdC 和 dC 的检测限均为1×10-5 mol／L。样品的甲基化程度以（5 mdC ）含量占总脱氧胞苷（5 mdC ＋ dC ）的比率表示。应用本方法分析小牛胸腺 DNA 的甲基化水平，结果为6.18％，与本研究组所得液质联用（LC-MS／MS）的定量结果（6.77％）和文献报导中应用液相色谱-紫外检测器（HPLC-UV）的检测结果（6.26％）对比，一致性好。结论本研究建立的方法分析速度快，准确性高，稳定性好，灵敏度满足微量样本的检测需求，可以用于临床甲基化诊断。
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