This paper reports the protein analysis by using microchip IEF carried on an automated chip system. We herein focused on two important topics of microchip IEF, the pH gradient and cathodic drift. The computer simulation clarified that the EOF could delay the establishment of pH gradient and move the carrier ampholytes (CAs) to cathode, which probably caused a cathodic drift to happen. After focusing, the peak positions of components in a calibration kit with broad pI were plotted against their pI values to know the actual pH gradient in a microchannel varying time. It was found that the formed pH gradient was stable, not decayed after readily steady state, and migrated to cathode at a rate of 10.0 mu m/s that determined by the experimental conditions such as chip material, internal surface coating and field strength. The theoretical pH gradient was parallel with the actual pH gradient, which was demonstrated in two types of microchip with different channel lengths. No compression of pH gradient was observed when 2% w/v hydroxypropyl methyl cellulose was added in sample and electrolytes. The effect of CAs concentration on current and cathodic drift was also explored. With the current automatic chip system, the calculated peak capacity was 23-48, and the minimal pI difference was 0.20-0.42 for the used single channel microchip with the effective length of 40.5 mm. The LOD for the analysis of CA-I and CA-II was around 0.32 mu g/mL by using normal imaged UV detection, the detected amount is ca. 0.07 ng.