The objective of the research in this dissertation is to develop microsystem based separation technologies for whole cell cancer analysis using human whole blood as the input sample. This research work is carried out with two different approaches; one based on a miniaturized cascade magnetophoresis system and a second based on dielectrophoresis. The miniaturized systems can be fabricated using MEMS technologies combined with plastic fabrication techniques. The design, fabrication, packaging, and characterization of several versions of the magnetophoresis and dielectrophoresis microsystems for whole cell cancer analysis in human whole blood sample are presented. The developed magnetophoresis systems have demonstrated improved throughput in the removal of RBC from a human whole blood sample and its application to the separation of tagged cancer cells based on their surface expression level of a specific protein. The dielectrophoresis microsystem has successfully shown the ability to steer a blood stream between two outlets and to separate WBCs or cancer cells from a human whole blood sample. The developed microsystem based separation technologies can be further applied to the development of integrated system for cancer detection and treatments.