Diverse cell types are known to contribute to pathology in inflammatory diseases such as rheumatoid arthritis. Analyzing inflammatory disease-related alterations in gene expression in different cell types requires cell purification without influencing the gene expression profile. Magnetic cell sorting has become a standard method to isolate almost any cell type in complex cell mixtures such as peripheral blood. The major differences between the magnetic cell separation systems that are currently used are the composition and size of the magnetic particles used for cell labeling and the mode of magnetic separation. Large (0.5–5 μm diameter) magnetic particles have several disadvantages when compared to small (20–150 nm diameter) particles [1], including slower cell-bead reaction kinetics, a higher degree of non-specific cell-bead interaction, higher risk of non-specific entrapment of cells in particle aggregates, and adverse effects of particles on viability and optical properties of labeled cells. Here, we focus on applications of magnetic cell sorting with MACS® technology [1 2 3 4 5] that makes use of nanometer-size super-paramagnetic particles and high gradient magnetic fields.