A magnetic nanoparticle imaging system has driving coils driven at multiple frequencies, the driving coils positioned to provide magnetic fields and field gradients to an imaging zone, and a static bias field magnet positioned to provide a static magnetic field and/or field gradient to the imaging zone. Magnetic sensors are positioned to sense magnetic fields from the imaging zone, and a signal processor processes signals from the sensors to find at least signal magnitude and phase at harmonics and/or intermodulation products of the multiple frequencies. In embodiments, the signal processing apparatus also determines signal magnitudes and phase of at least second and third harmonics of the first frequency, and maps location of nanoparticles in the imaging zone based upon the magnitudes of harmonics and magnitudes of the intermodulation products.