PCR contamination inhibits legitimate target amplification. a) PCR to amplify mouse mitochondrial DNA was optimized to detect from 60 ng to 10 fg of mouse DNA. The reaction was intentionally contaminated with previously generated mouse mitochondrial DNA PCR product. b) The PSMA mouse transgene PCR was intentionally contaminated with PCR products from the mouse mitochondrial DNA PCR and the PSMA PCR. c) Mouse mitochondrial PCR product was diluted from 10-2 to 10-6. These dilutions were used to contaminate a subsequent mouse mitochondrial PCR. d) The PSMA PCR product was diluted from 10-2 to 10-10. The dilutions were used to contaminate a subsequent PSMA PCR. Human LNCaP DNA and water were run as negative controls and 60 ng of mouse DNA was used as a positive control. All PCR products, including the PCR products used to contaminate the reactions, were amplified with ABI Gene Expression Master-mix containing UNG. The results demonstrate inhibition of amplification of large copy numbers of legitimate PCR target when contamination with minute quantities of the same or different previously generated PCR product was present.