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Six blood groups (Rh, MN, Duffy, Kidd, Kell and Lutheran) were investigated among three major ethnic groups (Bosniaks, Bosnian Croats, and Bosnian Serbs) as well as ten regional subpopulations across Bosnia and Herzegovina (Krajina, Posavina, North-Eastern Bosnia, Eastern Bosnia, Middle Bosnia, Central Bosnia, Sarajevo Region, Eastern Herzegovina, Central Herzegovina, and Western Herzegovina). This is the first study that introduces the molecular genetic typing of five blood groups within the population of Bosnia and Herzegovina with the exception of RhD blood group. The sample consisted of 450 buccal swabs from unrelated individuals. Five blood group systems (RhD, RhC, RhE, Kidd, MN) were genotyped by the PCR-SSP method, while three blood group systems (Kell, Duffy, Lutheran) were genotyped by the PCR-RFLP method. Minor variation of genetic diversity was observed within the three major ethnic groups in B&H as well as within the ten subpopulations stratified according to geographical criteria. No genetic differentiation among ethnic groups was noticed. These results are in agreement with the results of previous studies based on different molecular genetics markers, which indicate that the three ethnic groups of Bosnia and Herzegovina belong to the same gene pool. A similar level of genetic variance was observed within regional subpopulations with no significant genetic differentiation among them. Comparison of intrapopulation genetic diversity of the Bosnian and Herzegovinian population with other European and non-European populations, based on the three loci (RHD, MN and KEL), clearly showed that the level of genetic diversity of the Bosnia and Herzegovina population is within the European range.