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This paper presents a microelectromechanical systems (MEMS) differential thermal biosensor integrated with microfluidics for metabolite measurements in either flow-injection or flow-through mode. The MEMS device consists of two identical freestanding polymer diaphragms, resistive heaters, and a thermopile between the diaphragms. Integrated with polymer-based microfluidic measurement chambers, the device allows sensitive measurement of small volumes of liquid samples. Enzymes specific to a metabolic analyte system are immobilized on microbeads packed in the chambers. When a sample solution containing the analyte is introduced to the device, the heat released from the enzymatic reactions of the analyte is detected by the thermopile. The device has been tested with glucose solutions at physiologically relevant concentrations. In flow-injection mode, the device demonstrates a sensitivity of approximately 2.1 muV/mM and a resolution of about 0.025 mM. In flow-through mode with a perfusion flow rate of 0.5 mL/h, the sensitivity and resolution of the device are determined to be approximately 0.24 muV/mM and 0.4 mM, respectively. These results illustrate that the device, when integrated with subcutaneous sampling methods, can potentially allow for continuous monitoring of glucose and other metabolites.