Applications of flow karyotype analysis and flow chromosome sorting are being developed and are becoming increasingly relevant to clinical research. Among these applications are the quantitative analysis of chromosomal DNA content changes enabling the detection of minute deletions or unbalanced translocations, the quantitative analysis of aneuploidy for trisomy screening, and the sorting of derivative chromosomes for mapping chromosome breakpoints. Flow karyotyping has been accomplished on samples with clinical relevance including peripheral blood from both children and cancer patients as well as amniotic cell cultures. New techniques in flow cytogenetics to resolve chromosomes by morphology or by DNA sequence hybridizations are assessed for their promise. Although flow karyotyping has not yet developed into an 'automated' karyotyping technique, when used in conjunction with classical cytogenetic techniques, new information of significance to the clinician can be produced.