This paper presents the development of a microsystem for whole blood purification and electrophysiological analysis of the purified cells. Magnetophoresis using continuous diamagnetic capture (DMC) was utilized for whole cell purification and electrical impedance spectroscopy (EIS) was utilized for electrophysiological analysis of the purified cells. The system was developed on silicon and plastic substrates utilizing conventional microfabrication technologies and plastic microfabrication technologies. Using the magnetophoretic microseparator, white blood cells were purified from a sample of whole blood. The experimental results of the DMC microseparator show that 89.7% of the red blood cells (RBCs) and 72.7% of the white blood cells (WBCs) could be continuously separated out from a whole blood using an external magnetic flux of 0.2 T. EIS was used as a downstream whole cell analysis tool to study the electrophysiological characteristics of purified cells. In this work, primary cultured bovine chromaffin cells and human red blood cells were characterized using EIS. Further analysis capabilities of the EIS were demonstrated by successfully obtaining unique impedance signatures for chromaffin cells based on the whole cell ion channel activity.