High gradient magnetic separation is a well-established technology in the mineral processing industry, and has been used for decades in the bioprocessing industry. Less well known is the increasing role that high gradient magnetic separation is playing in biomedical applications, for both diagnostic and therapeutic purposes. We review here the state of the art in this emerging field, with a focus on therapeutic haemofiltration, the key enabling technologies relating to the functionalisation of magnetic nanoparticles with target-specific binding agents, and the development of extra-corporeal circuits to enable the in situ filtering of human blood.