The ABO system is the most important blood group system in transfusion and transplantation medicine. Over the last decade ABO genotyping was introduced to complement serological analysis but because of the enormous diversity at the ABO locus, DNA-based typing is highly sophisticated. In some genotype combinations and especially when dealing with hybrid genes, cis/trans linkage analysis is necessary. Therefore, we developed a simple and reliable approach to isolate ABO haplotypes. The described method physically separates diploid genomic DNA using probe-dependent allele hybridization followed by magnetic bead separation. After this haplotype-specific extraction (HSE), sequencing based typing (SBT) was performed to analyze coding and non-coding respectively regulatory regions of ABO.