The ancient DNA community has responded to this challenge by developing a set of best-practice protocols that minimize contamination risk, detect contamination when it occurs, and authenticate genuine ancient sequences on the basis of their specific chemical characteristics.

Clean-room protocols are among the most important contamination controls.

Ancient DNA work is conducted in laboratory spaces that are physically separated from other molecular biology work, maintained at positive air pressure to prevent contaminant-bearing air from entering, regularly decontaminated with UV radiation and bleach solutions, and used exclusively by researchers wearing full protective equipment including gloves, masks, and full body coverage.

These precautions dramatically reduce the amount of modern human DNA that can enter the analysis environment.