A total of 280 unrelated males from the three largest population groups in Bulgaria: Bulgarians, Bulgarian Turks and Gypsies, were analyzed for seven Y-chromosome STRs (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393). Comparison of the allele frequency distributions revealed significant differences between the three ethnic groups which were confirmed with haplotype analysis. This permits us to suggest that population differentiation should be taken into account in forensic case analysis and paternity testing in Bulgaria.