GenPlex (Applied Biosystems) is a new SNP genotyping system based on an initial PCR amplification followed by an oligo ligation assay (OLA). The OLA consists of the hybridization of allele and locus specific oligonucleotides (ASOs and LSOs) to PCR products and posterior ligation of ASOs and LSOs. The ligation products are immobilized to microtitre plates and reporter oligonucleotides (ZipChute probes) are hybridized to the ligation products. ZipChute probes are subsequently eluted and detected using capillary electrophoresis. Applied Biosystems developed the GenPlex SNP genotyping system with amelogenin and 48 of the 52 SNPs used in the 52 SNP-plex assay developed by the SNPforID consortium. The system requires equipment that is usually found in forensic genetic laboratories. The use of a robot for performance of the pipetting steps is highly recommendable. A total of 286 individuals from Denmark, Somalia and Greenland were investigated with GenPlex using a Biomek 3000 (Beckman Coulter) robot. The results were compared to results obtained with an ISO 17025 accredited SNP typing assay based on single base extension (SBE). With the GenPlex SNP genotyping system, full SNP profiles were obtained in 97.6% of the investigations. Perfect concordance was obtained in duplicate investigations and the SNP genotypes obtained with the GenPlex system were concordant with those of the accredited SBE based SNP typing system except for one result in rs901398 in one of 286 individuals most likely due to a mutation 6 bp downstream of the SNP. Reproducible SNP genotypes were obtained from as little as 250 pg of DNA.