Stored surplus of dried blood spot (DBS) samples from neonatal screening programs constitute a vast potential for large genetic epidemiological studies. However, age of the samples and the small amounts of DNA available may limit their usage. In this study we validate genotyping accuracy and efficiency of whole-genome-amplified DNA (wgaDNA) obtained from stored DBS samples, with reference to fresh genomic DNA from the same individuals. DBS samples from 29 volunteers, stored for up to 25 years, in the Danish Neonatal Screening Biobank were included and three DNA extraction methods, each using one 3.2 mm disk, were evaluated. Four whole-genome amplification kits, and one re-amplification kit, were used. Thirty-one SNPs were genotyped using the Sequenom platform and the wgaDNA samples calls were compared with their references for accuracy and efficiency evaluation. The genotype calls done blinded by the user had in many setups a 100% call- and concordance rate. Our results showed that genotyping performance is dependent on the combination of extraction procedure and amplification method, whereas years of storage did not seem to influence in this study. Based on these results we conclude that DBS samples should be considered a reliable and potential resource for future genotyping studies.