Endurance performance depends on the integration of several phenotypic traits influenced by multiple environmental and genetic factors. Objectives of the study were: (1) to examine the genotypic frequencies of the ACE I/D, ACTN3 R577X polymorphisms and endurance performance-related phenotypes, (2) to evaluate the dynamics of endurance performance parameters during a 5-year period in relation to ACE I/D and ACTN3 R577X genotypes in Estonian young skiers. Determination of VO_2peak was performed in 58 skiers aged 15-19 years (41 males, 17 females) during a 5-year period. The control group consisted of 322 healthy non-athletic subjects (145 males, 177 females). The study groups were genotyped for the ACE I/D and ACTN3 R577X variants. Frequencies of the ACE ID and ACTN3 RR genotypes were significantly higher (p = 0.047 and p = 0.003, respectively) and the RX genotype was lower (p = 0.008) in young male skiers compared with controls. A significant relationship was found between change (Δ) of training volume and ΔVO_2peak (mL·kg^-1·min^-1) (r = 0.475, p = 0.002). No significant main effect was detected between VO_2peak (mL·kg^-1·min^-1) dynamics (comparison with the previous age group data) and ACE I/D and ACTN3 R577X genotypes interactions (F = 0.571, p = 0.770 and F = 0.650 and p = 0.705, respectively) in all young skiers. Study results indicated a significantly higher frequency of the ACE ID and ACTN3 RR genotypes among Estonian young male skiers compared with the male control group. Significant genotype-related differences in dynamics of VO_2peak during a 5-year period were not found. In the future, longitudinal research including different gene variants may contribute to a better understanding of the nature of endurance performance.

• Significantly higher prevalence of the ID and the RR genotypes were found among Estonian young male skiers compared with the male control group, which may be an advantage for the explosive speed and power capacity in race skiing.

• A more remarkable trend of increase in VO_2peak (mL·kg^-1·min^-1) during the 5-year period was observed among male skiers with the XX genotype and among female skiers with the ID genotype.

• No significant genotype-related associations in the dynamics of VO_2peak were found during the 5-year period.