Generally, DNA markers used for individual analysis are based on repeat sequences. An alternative to using the repeat sequences as markers is the use of SNPs, which have an advantage in that SNPs are able to be used on poor or degraded samples which may be all that is available. The current study analyzed the typing and information content of a panel of 41 SNP samples by primer extension (PEX) and Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). SNP samples were selected for their conservation, lack of phenotypic expression, and frequency of occurrence in populations. Thirty-six autosomal SNPs were used to genotype 21 inclusionary and 3 exclusionary paternity cases. Additionally, the behavior of 5 X-chromosome SNPs was analyzed in a French population. The autosomal SNPs indicated independent inheritance and gave clear paternity results. All the X-chromosome SNPs were useful as both paternity and identification markers and PEX and MALDI-TOF MS proved a powerful method for the exploitation of biallelic markers. Tables, figures, references