Introduction We aimed to test the hypothesis that a combination of genetic variations forming a polygenic profile could estimate high and low responders to exercise-induced muscle damage (EIMD). Methods Sixty-five young female and male untrained Caucasians performed 120 maximal eccentric knee-extensions to induce EIMD. Maximal quadriceps strength, range of motion (ROM), muscle soreness and serum blood biomarkers were assessed before, directly after and 48 h after the EIMD intervention and participants were genotyped for 20 candidate single nucleotide polymorphisms (SNPs). Significant SNPs were further investigated regarding the muscle recovery following an artificial wound healing assay in vitro. SNPs that showed a gene-intervention interaction in vivo, were used to calculate a total genotype score in respect to the acute response following EIMD (TGS-A) and the cohort was then divided into a “preferential” (PG), “moderate” (MG), and “non-preferential” (NPG) genetic group. Results Four SNPs, which showed an interaction/main effect with the EIMD-intervention in vivo, also demonstrated changes in muscle stem cell characteristics in vitro. Seven SNPs demonstrated significant interactions in vivo, and these candidate SNPs were used to compute the TGS-A. There was a main effect for isometric and isokinetic MVC torque regarding TGS-A (both P<0.001). Individuals of the NPG and MG group were consistently weaker compared to the PG group (P=0.005), and NPGs demonstrated higher muscle soreness (P=0.003) and decreased ROM (P=0.006) following the EIMD-intervention, respectively. Conclusion Seven SNPs have been associated with EIMD and recovery. When SNPs were combined, NPG not only demonstrated poorer recovery following EIMD but this group was also generally weaker than PG, which could have clinical implications in terms of exercise prescription for reducing injury risk in those who are predisposed to greater muscle damage following strenuous exercise. Further, the associations between four of these seven SNPs with in vitro damage/regeneration suggest novel gene-cell-skeletal muscle mechanisms explaining the individual response to EIMD.