Block matching is a valuable tool for selecting donors for bone marrow transplantation. Identical, electrophoretic profiles of unrelated bone marrow donor-recipient pairs have been shown to be associated with long-term survival and a reduction of graft versus host disease (GVHD). This study was undertaken to determine the sequences of the PCR products which are generated. PCR products obtained with beta-block primers following the amplification of DNA extracted from cell lines homozygous for 7.1 and 8.1 ancestral haplotypes were cloned and sequenced. The PCR products were characterised and the beta block profiles reconstructed. The data indicate that the profiles consist of homoduplexes and heteroduplexes which are formed by the products of probably 3 different sequence locations.