Abstract: This invention provides a method of detecting pathogens comprising the steps of: (a) contacting a sufficient amount of biofunctional magnetic nanoparticles with an appropriate sample for an appropriate period of time to permit the formation of complexes between the pathogens in the sample and the nanoparticles; (b) using a magnetic field to aggregate said complexes; and (c) detecting said complexes. The method may further comprise the additional step of removing said complexes. The biofunctional magnetic nanoparticles are preferably a conjugate of vancomycin and FePt. The pathogens may be bacteria or viruses, and the sample may be a solid, liquid, or gas. Detection may involve conventional fluorescence assay, enzyme-linked immunosorbent assay (ELISA), optical microscope, electron microscope, or a combination thereof. The sensitivity of detection for the method is at least as low as 10 colony forming units (cfu) of the pathogens in one milliliter of solution within one hour.