DNA isolated from saliva has become an attractive alternative to the use of blood-derived DNA in genetic studies and is now extensively used in many applications. This review addresses advantages of saliva DNA for large population-based studies and points out caveats for use in certain techniques. We compiled data comparing saliva-derived genomic DNA to blood-derived DNA with regards to quality, quantity and convenience. Special attention is given to the usefulness of saliva-derived DNA for PCR-based methods and genome-wide analyses.