A comparative study of extracellular DNA versus genomic or apoptotic DNA was executed by fluorescent in situ hybridization (FISH) analysis. Extracellular DNA from culture medium and bound to the cell surface of human primary endotheliocytes, human primary fibroblasts and HeLa cells were investigated. There were not any specific peculiarities found in extracellular DNA isolated from the culture medium of endotheliocytes and HeLa cells. We revealed an overrepresentation of chromosome 9 fragments and the regions of the short arms of chromosomes 13, 14, 15, 21, 22 in DNA isolated from the culture medium of primary fibroblasts. The pericentromeric region of chromosome 9 is also overrepresented in cell surface bound DNA isolated from endotheliocytes, fibroblasts and HeLa cells. The data obtained allow a rational selection of DNA targets for the investigation of extracellular DNA generation and circulating DNA-based diagnostics.