Regular exercise training brings about desirable physical effects, including an increase in both endurance capacity and muscle strength/volume and an improvement in arterial stiffness that regulate blood pressure. However, these effects vary greatly between individuals. In addition to environmental factors, the genetic backgrounds causing those individual variations are inferred. Research exploring genes which regulate physical capabilities and training-induced effects is widely being implemented. These studies will encourage an individually tailored prescription of lifestyle/exercise for health. This review focused on individual variations of exercise training-induced effects on physical endurance capacity, muscle strength/volume and arterial stiffness. The relation between these effects and the gene and genetic factors, and future perspectives were discussed. Concerning endurance capacity, many studies have been carried out on ACE genotype, and also the relation to polymorphisms of mtDNA, UCP gene or HIF1A gene. In our studies, the polymorphisms of mitochondria-related genes were explored, revealing a suggestion that polymorphism is related to the endurance capacity and the phenotypes in skeletal muscles. Regarding muscle strength and volume, polymorphisms in myostatin, AMPD and CNTFR have been investigated. Our study observed genes that indicated expression dynamics related to exercise training effects on muscle strength and volume. As a result of investigation of genes concerned with arterial stiffness improvements by exercise training, changes in many gene expressions were found. Moreover, using the genes regulated by the training as candidates, training-induced effects on arterial stiffness and polymorphisms of these candidate genes were studied. The results suggest the possibility of genetic factors influencing training-induced effects on arterial stiffness. Genetic factors are clearly involved in exercise training-induced effects on endurance capacity, muscle strength/volume and arterial stiffness. Considering the effects of exercise training, the time is approaching when genetic factors will be taken into consideration.