Chromosome analysis and sorting by flow cytometry continues to open new avenues for the detection and analysis of chromosome and genetic rearrangements, the search for DNA sequence probes linked to genetic diseases, gene mapping, and genome organization. Our aims are to: resolve individual chromosome types, detect genetic rearrangements, improve methods of chromosome sorting, develop a new techniques for ultrahigh speed sorting, and analyze and sort chromosomes for the biomedical research community. These aims are based on a careful evaluation of current and future chromosome sorting requirements and indicate a clear need for sorting large quantities of chromosomes (for large insect vectors: YACs, BACs, and others) as well as sorting small numbers of chromosomes from many species for specialized applications (cloning break points, constructing linker-adapter libraries, and reverse chromosome painting). New capabilities will be forthcoming with new monochromosomal somatic cell hybrids and labeling with chromosome- specific antibodies. Sorting individual mouse chromosomes will be emphasized to help meet the needs of the mouse genetics community. Four approaches to resolve the mouse genome are planned. The sorting process itself will benefit from 1) a new optical sorter, 2) a new digital data acquisition system, and 3) field-flow fractionation. The optical high speed sorter will rely on "chromosome inactivation" by photosensitizing and cross-linking metaphase chromosomes. By eliminating the need to create droplets, sorting rates will be achieved which are 50 to 100 times faster than commercial sorters.