The preparation and application of rod-shaped core-shell structured Fe(3)O(4)-Au nanoparticles for immunomagnetic separation and sensing were described for the first time with this study. To synthesize magnetic gold nanorod particles, the seed-mediated synthetic method was carried out and the resulting nanoparticles were characterized with transmission electron microscopy (TEM), ultraviolet visible spectroscopy (UV-Vis), energy-dispersive X-ray (EDX), and X-ray diffraction (XRD). Magnetic properties of the nanoparticles were also examined. Characterization of the magnetic gold nanorod particles has proven that the resulting nanoparticles were composed of Fe(3)O(4) core and the gold shell. The rod-shaped gold-coated iron nanoparticles have an average diameter of 16 +/- A 2 nm and an average length of about 50 +/- A 5 nm (corresponding aspect ratio of 3). The saturation magnetization value for the magnetic gold nanorod particles was found to be 37 emu/g at 300 K. Rapid and room temperature reaction synthesis of magnetic gold nanorod particles and subsequent surface modification with E. coli antibodies provide immunomagnetic separation and SERS application. The analytical performance of the SERS-based homogenous sandwich immunoassay system with respect to linear range, detection limit, and response time is also presented.