This paper reports an automated polymer based microfluidic analysis system integrated with a surface plasmon resonance (SPR) biosensor that demonstrates the detection of specific binding of biomolecules and that qualitatively monitors cell adhesion on the sensor surface. Micropumps, microchannels, and an SPR biosensor were integrated into a single polymer (PMMA) based microfluidic system. The integrated system has been studied for its potential applications in bio-molecules detection and drugs discovery. Two experiments, (1) monitoring the reaction between the BSA-BSA antibody, and (2) monitoring the activities of living cells in the presence or absence of trypsin in a RPMI-1640 medium, were conducted to show the biomedical application capability. Because SPR based bio-detection requires optically transparent substrates, PMMA is a potential replacement for glass and silicon-glass in microfluidic systems, if bio-compatibility and low-cost are desired. Hence, our work has shown the feasibility of commercializing an SPR based bio-medical/chemical analysis system in the near future.