The term “magnetophoresis” has been proposed to describe the behavior of a magnetic particle moving through a viscous medium under the influence of an external magnetic field. Its origin can be traced to a similar term used to describe particle motion in a viscous medium under the influence of an electric field, “electrophoresis.” The number of publications on magnetophoresis has rapidly increased during the last 10 years primarily due to a burgeoning interest in its applications to biomedical research and clinical diagnostics and therapy. The appealing feature of magnetophoresis is that under well‐controlled conditions it provides a means for gentle cell separation in its natural milieu that could be both highly specific and highly sensitive at a relatively low cost with respect to the separation equipment. The increasing interest in single‐cell biology in health and disease and the rapidly improving sensitivity of molecular biology methods in applications to single‐cell genomic analysis put a special emphasis on high quality, high volume, and relatively inexpensive cell separation methods, such as those provided by cell magnetophoresis in microfluidic channels. The growth in magnetophoresis research and applications is aided by a synergy between materials science, nanoparticle synthesis and characterization, micro‐ and nanofluidic engineering, experimental and computational fluid dynamics research, and physics of high magnetic fields. This leads to emerging applications, such as detection of paramagnetic impurities in diamagnetic samples and biomagnetic cell separations. These are areas of magnetophoresis applications that will likely continue to rapidly grow.