During migration toward gonadal ridges, primordial germ cells (PGCs; the earliest identifiable germ cells in the embryo) are very few in number, move along different tissues, and are not identifiable by morphological criteria alone. Here we report the use of the magnetic cell sorter MiniMACS as a tool for the isolation of such rare cells from 10.5- to 13.5-days post coitum mouse embryos. Cells stained sequentially by TG-1 (a monoclonal IgM antibody known to bind to the surface of PGCs) and superparamagnetic microbeads coated with secondary anti-mouse IgM antibody were separated on a magnetic column. Unlabeled cells (somatic cells) pass through the column, while labeled cells (germ cells) are retained. The retained cells can be eventually easily eluted and immediately used for biochemical studies or grown in suitable in vitro culture systems.