Phosphatidylcholine of high purity (PC, content 92.80%) was prepared from market soybean power phospholipids (PC content 14.05%) by using solvent extraction and column chromatography. As the main objective, micellar electrokinetic capillary chromatography (MECC) was established for the separation and analysis of phospholipids. MECC conditions such as surfactant and its concentration, pH of running buffer solution, organic modifier and its volume content, concentration of buffer solution, temperature etc were optimized to provide good separation and larger peak area of phospholipids. The optimum MECC conditions were as follows: running buffer system of 35 mmol/L sodium deoxycholate (SDC)-1 mmol/L borax buffer solution/n-propanol (57 : 43, v/v) with pH 8.30, column temperature of 44 degrees C, applied voltage of 25 kV and ultraviolet (UV) detection at 200 nm. Addition of standards was used to identify the components of phospholipids. External standard method was used to determine PC content. As the results shown, five components of phospholipids could be effectively separated under the optimum MECC conditions. Correlation coefficient within 0.1 - 1 g/L PC concentration reached 0.999 0. The average recovery of PC was 98.0%. The intra-day relative standard deviation (RSD) and inter-day RSD of peak area of PC were 1.36% and 3.27%, respectively. The qualitative result of PC obtained by MECC was consistent with that determined by thin layer chromatography and infrared analysis, respectively. So MECC can be used as an effective tool for the separation, analysis and quality control of phospholipids.