We adapted the PCR method to screen up to 3,000 blood donations per day for HBV, HCV, and HIV-1 contamination. Concerning logistics: The first step is the generation of 3 identical microtiter plates (PT) by using the self-validated automatic sample processor with disposable tips. Using the first PT, we pooled up to 600 aliquots taken from blood donations which are serological negative and free for clinical usage according to actual federal regulations. In the case of a positive PCR pool result the viremic donation is identified by 2 additional PCR pool testing steps with smaller pool sizes using the second and third PT. All described steps are supported by electronic data processing. The PCR-method: After virus concentration by ultracentrifugation and--in case of HCV and HIV-1--additional reverse transcription PCR-amplifications were performed. PCR in two genomic regions are done for each virus. Laser-induced fluorescence detection after polyacrylamide gel electrophoresis and computer analysis were used to check the amplification products. Using this approach, a virus-containing donation can be detected in up to 599 negative samples with following sensitivity: HBV and HIV-1, 1,000-1,500 genome equivalents/ml; HCV, 2,000-2,500 genome equivalents/ml, thus sensitivity being in the range of commercial available PCR kits when testing nonpooled samples. The sensitivity was validated by using national and international available standards with known virus genome concentrations. All processing steps are checked using different controls such as, e.g., negative, positive, premix controls, reporter virus, inhibition controls. Routinely employing this validated methodology, we investigated 327,013 donations until the end of June 1996. During this survey, we found at least 16 virus-containing donations which are negative in corresponding serological tests and would have been transfused (4 HBV-, 13 HCV-, 0 HIV-1-containing donations), including one later seroconversion for HBV and one for HCV. Using our adapted PCR-methodology, it seems possible to shorten the diagnostic window periods with acceptable costs for large transfusion centers (15 DM per donation for all 3 viruses including all steps and investments). Therefore, PCR seems to become a new method of choice to prevent transfusion transmitted infections.