Magnetic nanowires (MNWs) were explored as potential magnetic tags for cell detection with giant magnetoresistance (GMR) biosensors based on a handheld system. Due to size, shape anisotropy and higher moment materials, the signal detected from a single MNW was 2500 times larger than that from a single magnetic iron oxide nanobead, which is important for ultra-low concentration cell detection. A model was used to determine how the MNW orientation with respect to the GMR sensor impacts detection performance, and the results aligned well with the experimental results. As a proof of concept OSCA-8 cells tagged with Ni MNWs were also detected using the same handheld system. The limit of detection (LOD) in aqueous solution appeared to be 133 cells, and single-cell detection can be realized if the cell is in direct contact with the sensor surface. Since MNWs are already employed in magnetic separation of cells, directly using MNWs as tags in cell detection eliminates the need of additional functionalization with other labels. This largely simplifies the detection process and reduces the risk of contamination during sample preparation.