The demonstration that CD T-cell counts can be used to monitor HIV disease progression opened the way to the first clinical application for fluorescence activated cell sorting (FACS) technology. Modern FACS methodologies such multicolor staining and sorting has opened the way to new and constructive therapeutic and clinical applications. This article outlines approaches in which current users can use to improve the quality of their FACS work without undue effort. FACS technology development and the emergence of new software support for this technology are cooperating in this effort.