Objectives: Studies in recent decade demonstrated the importance of HDL subfractionation in precision medicine. It is notable that not all HDL subfractions are “good” lipoprotein. The lack of a reliable technique that can precisely identify each particle of HDL subfractions remains the major obstacle in clinical application. Based on the principle of microfluidic electrophoresis, we have developed an automatic system (MFE) that meets the need of clinical applications. The objectives of this paper is to test the system for its application, precision, and also the normal range in healthy population using one of major subfraction, HDL-2b, as a target. Methods: The MFE was compared with traditional non-denaturing polyacrylamide gradient gel electrophoresis (GGE). Intra-chip, inter-chip, inter-instrument, inter-lab, and inter-operator precisions were all tested by using the sample in various conditions. An instruction was provided with the instrument and HDL subfractioning kit. Data were analyzed with SPSS for correlation of variation, regressions, etc. Results: The new system exhibited a linear correlation with the traditional GGE system. The intra-chip %CVs, inter-chip %CVs, inter-instrument %CVs of HDL-2b were less than 10%, which was the set acceptance criteria. With 243 samples from healthy individuals demonstrated that the mean value of HDL-2b% is about 25% in both male and female. Conclusions: Our data demonstrated that the MFE system is a fast, automatic, and reliable system that can obtain the percentage of HDL-2b with high precision