Nucleotide sequencing of approximately 400 basepairs upstream from exon 1 of the DPB1 gene and sequence specific oligonucleotide hybridisation identified eight nucleotide positions to be polymorphic which were in linkage disequilibrium (LD) with DPA1 and DPB1 alleles. Substitutions at two sites (-230 and -224) formed three genotypes (DP-PRO1-3). DP-PRO 1 was the most common genotype and was in LD with DPA1*0103, *0202 and DPB1*0401, *0501. DP-PRO 2 was observed in LD with DPB1*02012, *1601, *1701 and DPA1*0104. DP-PRO3 was in LD with DPB1*0901, *1001 and DPA1*0201. Electrophoretic Mobility Shift Assays (EMSA) performed with restriction enzyme fragments showed substitutions at -230 and -224 not to be involved in binding nuclear proteins. Six substitutions were found on a single genotype (DP-PRO4) which was observed in seven samples; 67% of DP-PRO4 inferred haplotypes were HLA-A2-B46, DRB1*0901, DQB1*03032, DPA1*0401, DPB1*1301. Three of the substitutions occurred in conserved regulatory region boxes, W', X and Y, and three in the signal and leader sequences. EMSA competitive binding assays performed with oligonucleotide probes for the substitutions showed no difference in binding affinity for W' and X probes. The DP-PRO4 Y box had a decreased nuclear protein binding affinity compared to DP-PRO1-3. Whether the sum of the differences in DP-PRO4 relate to a change in the cell surface expression of HLA-DP is yet to be determined.