In this article, we report a MOSFET-type biosensor assembled in a polydimethylsiloxane (PDMS) micro-fluidic channel for the electrical detection of nano-scale biomolecules. The MOSFET-type sensor was fabricated on the basis of standard complementary metal oxide semiconductor (CMOS) technology. Au which has a chemical affinity with thiol by forming a self-assembled monolayer (SAM) was used as the gate metal. In order to apply to the hybrid micro-flow-system for a prototype lab-on-a-chip, the PDMS layer with the micro-channel was aligned along with the sensing area of the MOSFET device. Thiol which was injected into the micro-fluidic channel was detected by measuring the electrical characteristics of the MOSFET sensor in both ex-situ and in-situ due to the negative charge of thiol.