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This paper presents the detection of magnetic nanoparticles flowing into a microchannel using giant magnetic impedance (GMI) microwire sensor made up of CoFeSiBNb alloy (40 μm diameter and 1 cm long wire). Detection tests were performed using UltraSmall Particles of Iron Oxyde (USPIO) with diameter of 20 nm. Detection of volume of 180 nl with a concentration of 18 mmol (Fe)/l and flow rate of 260 nl/s was performed. Such type of measurement can find application in biomedical and clinical diagnosis for in vivo noninvasive detection.