Research involving cell analysis frequently requires isolation of certain cell types or subcellular components either as a final objective or as a preparative tool for further assays. At present, there are a high number of cell sorting methods that are suitable for being used in the clinical laboratory. These methods can be divided into two major groups: (1) bulk sorters and (2) single-cell-based sorters. This latter group mainly refers to fluorescence-activated cell sorting (FACS) by flow cytometry (FCM). In both cases, separation of cell subsets is based on their classification according to one or more cell characteristics. In bulk sorters, cell classification and sorting are usually achieved in a single step; by contrast, in FACS techniques, these two steps are independent sequential processes. In addition, bulk sorters generally use a single-cell characteristic to isolate cell subsets and have a higher throughput rate, as compared with FACS by FCM, where several parameters can be used simultaneously to classify cells for their further isolation. As a consequence of the mechanisms underlying these two cell sorting methods, the balance between cell purity and cell recovery on the sorted fraction are generally different, the single-cell-based methods usually providing both a higher purity and recovery. Thus, in practice, bulk separation methods are frequently used either as a preparative step for FCM-based cell sorting or for the enrichment of the sample in specific cell subsets, when a higher throughput rate is required; in contrast, FACS by FCM is selected for the isolation of cell subsets when a high purity and, especially, recovery of a specific subpopulation of cells present in a sample are needed.