Cells from individuals with genetic diseases ataxia telangiectasia (AT) and Fanconi anemia (FA) exhibit hypersensitivity to ionizing radiation (AT) or DNA cross-linking agents (FA) which may be caused by multiple factors including defects in chromatin structure and DNA repair. In this study, a combination of cytometric techniques was employed to study the chromatin conformation of AT and FA cells. Nuclei of peripheral blood mononuclear cells (PBMCs) and of skin fibroblasts established from AT and FA patients were analyzed by light scattering and fluorimetric titration with the DNA-intercalating dye propidium iodide. The light scatter measurements revealed the presence of small-sized nuclei with reduced granularity in PBMCs and fibroblasts from both AT and FA patients. The fluorometric titration data could be interpreted by assuming two classes of propidium iodide binding sites with different affinities. The number of high-affinity sites in AT and FA fibroblasts was significantly larger (by 20%) than in control cells. Our findings show the applicability of cytometric techniques for the rapid assessment of chromatin conformation and also suggest the possibility to identify AT and FA carriers.