Flow cytometry is an advanced technology that relies on the idea that certain fluorescent probe-labeled cells would scatter light and emit fluorescence when they move across a laser beam. Given that it enables quick, comparatively quantitative, multiparametric examination of cell populations on a single-cell basis, it has a number of special benefits. It also makes it possible to physically sort the cells in order to divide the subpopulation according to various criteria. Due to the great sensitivity and precision of this technology, research in the subject of flow cytogenetics, which is the analysis and sorting of chromosomes using flow cytometric techniques, has increased during the past 40 years. Nucleic acid-specific fluorescent dyes have reduced the subjectivity of previous slide-based approaches by enabling partially automated quantitative chromosomal analysis. Cell cycle analysis is still a developing area among those who use flow cytometry due to the discovery of new technologies and more cell cycle phase markers. Chromosomal aberrations can be detected by flow cytometric categorization of chromosomes (flow karyotyping), and large-scale isolation of individual chromosome types is possible for chromosome genomics through flow sorting. This chapter discusses the uses, limitations, and potential future developments of flow cytometry in genotoxicity assessment.