Physical separation of either intact target cells or specific molecules from many environments can result in a suspension free of contaminating particles, nontarget cells and biological inhibitors and highly enriched in the target cells or molecules of interest. The processed sample will be ready for the next part of the overall experimental protocol; e.g., a culture step, or a molecular biological procedure, and greater confidence in a successful outcome will be achieved. A range of methods exist for whole-cell extractions from a variety of environments. Such methods may aim to obtain a clean suspension that is representative of the bulk cell population, or may aim to target specific cells. On occasion, it is necessary to obtain a clean bulk cell suspension prior to specific cell extraction. This chapter deals with the separation of specific cells, either intact or targeting a marker molecule of interest. Methods for intact cell separations include flow cytometric cell sorting (1 ), optical trapping (2 ), micromanipulation (3 ), dielectrophoresis (4 ), ultrasound sedimentation (5 ), sedimentation field-flow fractionation (6 ) and elutriation (7 ,8 ). The general applicability and the degree of selectivity that can be achieved for the cell selection varies with each method. Of special importance in the context of this book is the environment from which the samples are taken, and the presence of nontarget particulate material, which can easily foul sensitive instruments, clog filters or hamper microscopic observations. One approach that has proven feasible from environments as challenging as feces, plant tissue, or soil is the use of magnetic particle separation technology.