Recent developments in sequencing methods have enabled whole genome sequencing of several species and the available sequence information has allowed the development of high throughput genotyping chips. However, these genotyping methods require high quality DNA. The possibility to genotype samples based on DNA from non-invasive sources would permit retrospective genotyping of previously collected samples and also facilitate the analysis of large populations e.g. for genomic selection. In this study we have developed and evaluated different DNA preparation methods from porcine hair root follicles for high throughput genotyping with the PorcineSNP60 Genotyping BeadChip (Illumina). We describe a method for DNA extraction from porcine hair root samples, which produces results from high throughput genotyping with the same high degree of accuracy as previously reported for DNA extracted from sperm, blood or tissue samples. This method was used for the genotyping of 273 hair follicle samples. When the DNA concentration was > 30 ng/ìl all samples had the same high call rate ( > 99%) as sperm samples confirming the robustness of this DNA extraction method for high throughput genotyping. Our data also establishes the suitability of the PorcineSNP60 BeadChip for genotyping the Finnish Landrace population.;