Donor-recipient disparitiy of the minor histocompatibility antigen HA-1 is relevant for the development of graft-versus-host disease after HLA-matched sibling allogeneic bone marrow transplantation in HLA-A*0201-positive individuals. Two different alleles of HA-1 with a single amino acid polymorphism have been identified. Here we describe a time- and cost-efficient method for HA-1 typing of genomic DNA, using site-specific hybridization probes with the LightCycler. This method was compared with standard techniques as sequencing or allele-specific polymerase chain reaction (PCR) and proved to be specific, reliable and reproducible. We conclude that HA-1-subtyping using fluorescent-labeled oligonucleotides represents a attractive method for the screening of samples before allogeneic transplantation in HLA-A*0201-positive individuals.