The first statistical analysis of the French National Registry of volunteer bone marrow donors estimated the probabilities of haplotype frequencies separately for each of the 20 administrative regions of France. Here we propose to use donors' surnames to increase the accuracy of location of the donor's geographical origin. This approach allows us to estimate haplotype frequencies for administrative entities (90 departments) smaller than regions and to correct for bias resulting from recent mobility. We analysed 30,777 donors typed for HLA-A,B and 17,745 donors typed for HLA-A,B,DR,DQ. By using the donors' surnames, we identified common and rare haplotypes (those found in only one department) and estimated the degree of HLA polymorphism at the department level. We also identified departments with a distinctive genetic structure (for example, Paris, Corsica, Pyrenees and Meurthe-et-Moselle). By providing a more accurate geographical distribution of HLA polymorphisms in France, this study will enable us to optimise policies for recruiting bone marrow donors and to improve the fit between the donor file and patients' needs.