Isolation and separation of proteins is an important procedure in all areas of biosciences and biotechnology. Currently recombinant fusion proteins are produced routinely; in order to simplify their isolation from complex samples, magnetic separation techniques can be efficiently used. This short review paper shows examples of the most important fusion affinity tags and commercially available magnetic affinity and ion exchange particles enabling efficient capture of recombinant fusion proteins. A list of realized isolation procedures documents the efficiency of magnetic separation techniques.