We demonstrate the application of a spin valve giant magneto-resistance (GMR) integrated microfluidic sensor for the detection and quantification of superparamagnetic nanomarkers. A microfluidic channel containing the magnetic fluid, micro-conductors (MCs) for collection of magnetic markers and a spin valve GMR sensor for detecting the presence of magnetic stray field were integrated into a single chip and employed for detection of various concentrations of Nanomag-D beads of 250 nm diameter. The results show that the sensor is capable of detecting concentrations as low as 500 pg μl⁻¹ of Nanomag-D beads and quantifying them in a linear scale over a wide particle concentration range (1–500 ng μl⁻¹). Our study provides a novel platform towards the development of a portable lab-on-a-chip sensor.