In this paper, we describe an extended gate field effect transistor (EGFET)-based biosensor for the detection of streptavidin-biotin protein complexes in a silicon microfluidic channel. The connection between EGFET and micro-fluidic system could be achieved with the proposed device, offering merits of isolation between the device and solution, compatibility with the integrated circuit (IC) technology and applicability in the micro total analysis system (μ-TAS). The device was fabricated on the basis of the semiconductor IC fabrication and micro-electro mechanical system (MEMS) technology. Au was used as the extended gate metal to form a self-assembled monolayer (SAM) with thiol. The bindings of SAM, streptavidin and biotin were detected by measuring the electrical characteristics of the FET device.