Meaningful applications of magnetic nanoparticles (MNP) in biomedicine require the ability to quantify MNP in a variety of environments and biological materials (cells, tissue, and organs). Here we describe a method for the integral, noninvasive quantification of MNP. Our method is based on magnetorelaxometry (MRX), it relies on the detection of their magnetic stray fields which permeate practically unaltered virtually any biological material. MRX provides a specific signal which is not affected by dia- and paramagnetic signals from the biological matrix. We describe how to conduct the MRX experiments and use MNP-assisted gene transfection as the example. The quantification is based on the comparison of the MRX signal of a sample and an appropriate reference sample.