Although 80% of childhood acute lymphoblastic leukemia (ALL) cases are cured with current treatment protocols, exposure to chemotherapeutics or radiation therapy during a vulnerable period of child development has been associated with a high frequency of late adverse effects (LAE). Previous observations suggest important skeletal muscle size, density and function deficits in ALL survivors. Given that only a fraction of all patients will suffer from this particular complication, we investigated whether it could be predicted by genetic markers.  We analysed associations between skeletal muscle force (Fmax) and power (Pmax) and germline genetic variants from 1039 genes derived through whole-exome sequencing. Top-ranking association signals retained after correction for multiple testing were confirmed through genotyping, and further analysed through stratified analyses and multivariate models.  Our results show that skeletal muscle function deficit is associated with two common single nucleotide polymorphisms (SNPs) (rs2001616 =0.0002 (Pmax) and rs41270041 , =0.02 (Fmax)) and two rare ones located in the gene =0.001 (Pmax)). These associations were further modulated by sex, body mass index and risk groups, which reflected glucocorticoid dose and radiation therapy ( ≤0.02).  Occurrence of muscle function deficit in childhood ALL is thus strongly modulated by variations in the and genes, which could lead to personalized prevention strategies in childhood ALL survivors.