Using polymerase chain reaction (PCR) amplification, it is possible to analyze DNA from limited source template. This method has proved especially valuable in studies of ancient DNA and in forensic investigations. However, PCR reactions containing minimal or damaged source template are prone to contamination by DNA from a number of other sources. While standard protocols to prevent and/or detect contamination do exist, methods of eliminating contamination are needed to ensure the validity of results obtained. We present a method to eliminate sources of contamination in reagents and labware through the use of a DNase prior to PCR amplification without damaging even the minimal amounts of template present in ancient DNA samples. This method, suggested previously for forensics applications, appears to be effective in eliminating contamination without interfering with the amplification of ancient template.