Abstract: A method for subtractive hybridization of desired DNA sequences from two cell or tissue populations. cDNA from experimental cells or tissues is modified by incorporation of nucleoside analogs to prevent subsequent exonuclease attack. Hybridization of the experimental and control cDNA is performed using the phenol-emulsion reassociation technique. The hybridized DNA is incubated with exonucleases, resulting in degradation of all but the desired duplex DNA which may then be amplified. This technique may be used to isolate differentially expressed genes or gene fragments and will contribute to our understanding of pathological conditions and developmental regulation.