We have developed a system where double-stranded cDNA can be amplified using a synthetic ollgonucleotide primer and the polymerase chain reaction, generating cDNA libraries in vitro . Using a library subtraction strategy (1), scrapie and control brain in vitro cDNA libraries were used to identify sequences whose expression is modulated In scrapie infection. One of these sequences represents β–2 microglobulin, while the other two have not been previously described. The use of in vitro libraries offers increased speed and efficiency of construction, and their subtraction is more efficient and powerful, compared with the previous system (1).