In this study, magnetic poly(ethylene glycol dimethacrylate-N-methacryloyl-(L)-glutamic acid) (mPEGDMA-MAGA) particles were prepared by the dispersion polymerization in order to purify thrombin effectively. mPEGDMA-MAGA particles were synthesized by adding different ratios of magnetite (Fe3O4) to the medium in addition to the monomer phases EGDMA and MAGA. The characterization studies of mPEGDMA-MAGA particles were used by fourier transform infrared spectroscopy, zeta size measurement, scanning electron microscopy and electron spin resonance. mPEGDMA-MAGA particles were used in thrombin adsorption studies from aqueous thrombin solutions in both batch and magnetically stabilized fluidized bed (MSFB) system. Maximum adsorption capacity in pH 7.4 phosphate buffer solution is 964 IU/g polymer and 134 IU/g polymer in MSFB system and batch system, respectively. The developed magnetic affinity particles enabled the separation of thrombin from different patient serum samples in one step. It has also been observed that magnetic particles can be used repeatedly without significant reduction in adsorption capacity.