Methods for separating magnetic nanoparticles are provided. In certain embodiments, a method is provided for separating magnetic nanoparticles comprising: providing a sample comprising a plurality of magnetic nanoparticles; passing the sample through a first magnetic field; at least partially isolating nanoparticles of the first nanoparticle size desired; altering the strength of the first magnetic field to produce a second magnetic field; and at least partially isolating nanoparticles of the second nanoparticle size desired.