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In a study of the Bosnian-Herzegovinian (B&H) population, Y chromosome marker frequencies for 100 individuals, generated using PowerPlex® Y23 kit, were used to perform Y chromosome haplogroup assignment via Whit Athey’s Haplogroup Predictor. This Whit Athey’s algorithm determines Y chromosome haplogroups from Y chromosome short tandem repeat (Y-STR) data using Bayesian probability-based approach. According to the results of the present study, the most frequent haplogroup appears to be I2a, with a prevalence of 49%, followed by R1a and E1b1b, each accounting for 17% of all haplogroups within the population. Remaining haplogroups encountered in this study are J2a (5%), I1 (4%), R1b (4%), J2b (2%), G2a (1%) and N (1%). These results confirm previously published preliminary B&H population data published over 10 years ago, especially the prediction about B&H population being a part of the Western Balkan area, which served as the Last Glacial Maximum refuge for the Paleolithic human European population. Furthermore, the results corroborate the hypothesis that this area was a significant stopping point on the “Middle East-Europe highway” during the Neolithic farmer migrations. Finally, since these results are almost completely in accordance with previously published data on B&H and neighboring populations that were generated by Y chromosome single nucleotide polymorphism (Y-SNP) analysis, it can be concluded that in silico analysis of Y-STRs is a reliable method for approximation of the Y chromosome haplogroup diversity of an examined population.