We characterized the magnetic markers used in biological immunoassays based on Brownian relaxation. Because the markers are composed of aggregated nanoparticles, i.e., magnetic nanoclusters, we first clarified their magnetic properties using AC susceptibility measurements, magnetization (M-H) curves, and magnetic relaxation properties. Analyzing the experimental results, we obtained the key parameters for the immunoassay, i.e., hydrodynamic diameter d(h), magnetic moment m(B), and anisotropy energy E-B of the markers. Because these parameters were distributed in practical samples, we took their distribution into account in the analysis. Next, we showed the relationship between these parameters obtained from different samples. It was shown that m(B) increased approximately in proportion to d(h). On the other hand, no clear correlation between m(B) and E-B was obtained. These results were very different from those expected from single-domain nanoparticles and must be taken into account when magnetic markers are used in immunoassays based on Brownian relaxation. (C) 2012 The Japan Society of Applied Physics