Small magnetic nanoparticles with a narrow size distribution are of great interest for several biomedical applications. When the size of the particles decreases, the magnetic moment of the particles decreases. This leads to a significant increase in the separation time by several orders of magnitude. Therefore, in the present study the separation processes of bionized nanoferrites (BNF) with different sizes and concentrations were investigated with the commercial Sepmag Q system. It was found that an increasing initial particle concentration leads to a reduction of the separation time for large nanoparticles due to the higher probability of building chains. Small nanoparticles showed exactly the opposite behavior with rising particle concentration up to 0.1 mg(Fe)/ml. For higher iron concentrations the separation time remains constant and the measured Z-average decreases in the supernatant at same time intervals. At half separation time a high yield with decreasing hydrodynamic diameter of particles can be obtained using higher initial particle concentrations.