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The role of genetics, as an intrinsic factor, in research of sports performance increases with every passing year. The polymorphism rs970547 of the COL12A1 gene is one of the most promising genetic markers linked to soft-tissue injuries. This study aimed to investigate whether COL12A1 rs970547 genotypes are associated with elite Lithuanian athletes from high-risk various sports, such as running, throwing, jumping, and football. The study involved 293 Lithuanian elite athletes and 287 healthy untrained individuals from the Lithuanian population. The results of this study suggest that the rs970547 T allele and TT genotype were significantly over-represented in the total athlete group compared to controls (p < 0.05). There was a significantly lower C allele frequency in the sprint/power group (16.9%) as well as in footballers (19.4%) compared to controls (33.3%, p < 0.05). Positive selection analysis results showed that the derived allele experiences selection pressure within the general population of Lithuanians. Taken together, the findings of this study suggested that COL12A1 rs970547 (T allele and TT genotype) is associated with elite athlete status, especially with sprint/power athlete and footballer`s performance. However, larger-scale studies within different ethnic backgrounds are still warranted to confirm the findings of our study.